diff --git a/src/components/NotificationRow.tsx b/src/components/NotificationRow.tsx
index c69f29d79..1f0752f22 100644
--- a/src/components/NotificationRow.tsx
+++ b/src/components/NotificationRow.tsx
@@ -10,7 +10,10 @@ import { AppContext } from '../context/App';
 import { Opacity, Size } from '../types';
 import type { Notification } from '../typesGitHub';
 import { cn } from '../utils/cn';
-import { formatForDisplay } from '../utils/helpers';
+import {
+  formatForDisplay,
+  isMarkAsDoneFeatureSupported,
+} from '../utils/helpers';
 import {
   getNotificationTypeIcon,
   getNotificationTypeIconColor,
@@ -126,16 +129,18 @@ export const NotificationRow: FC<INotificationRow> = ({
 
       {!animateExit && (
         <HoverGroup>
-          <InteractionButton
-            title="Mark as Done"
-            icon={CheckIcon}
-            size={Size.MEDIUM}
-            onClick={() => {
-              setAnimateExit(!settings.delayNotificationState);
-              setShowAsRead(settings.delayNotificationState);
-              markNotificationDone(notification);
-            }}
-          />
+          {isMarkAsDoneFeatureSupported(notification.account) && (
+            <InteractionButton
+              title="Mark as Done"
+              icon={CheckIcon}
+              size={Size.MEDIUM}
+              onClick={() => {
+                setAnimateExit(!settings.delayNotificationState);
+                setShowAsRead(settings.delayNotificationState);
+                markNotificationDone(notification);
+              }}
+            />
+          )}
           <InteractionButton
             title="Mark as Read"
             icon={ReadIcon}
diff --git a/src/components/RepositoryNotifications.tsx b/src/components/RepositoryNotifications.tsx
index 27b50ad49..c4aaab81c 100644
--- a/src/components/RepositoryNotifications.tsx
+++ b/src/components/RepositoryNotifications.tsx
@@ -10,6 +10,7 @@ import { AppContext } from '../context/App';
 import { Opacity, Size } from '../types';
 import type { Notification } from '../typesGitHub';
 import { cn } from '../utils/cn';
+import { isMarkAsDoneFeatureSupported } from '../utils/helpers';
 import { openRepository } from '../utils/links';
 import { HoverGroup } from './HoverGroup';
 import { NotificationRow } from './NotificationRow';
@@ -80,18 +81,20 @@ export const RepositoryNotifications: FC<IRepositoryNotifications> = ({
 
         {!animateExit && (
           <HoverGroup>
-            <InteractionButton
-              title="Mark Repository as Done"
-              icon={CheckIcon}
-              size={Size.MEDIUM}
-              onClick={(event: MouseEvent<HTMLElement>) => {
-                // Don't trigger onClick of parent element.
-                event.stopPropagation();
-                setAnimateExit(!settings.delayNotificationState);
-                setShowAsRead(settings.delayNotificationState);
-                markRepoNotificationsDone(repoNotifications[0]);
-              }}
-            />
+            {isMarkAsDoneFeatureSupported(repoNotifications[0].account) && (
+              <InteractionButton
+                title="Mark Repository as Done"
+                icon={CheckIcon}
+                size={Size.MEDIUM}
+                onClick={(event: MouseEvent<HTMLElement>) => {
+                  // Don't trigger onClick of parent element.
+                  event.stopPropagation();
+                  setAnimateExit(!settings.delayNotificationState);
+                  setShowAsRead(settings.delayNotificationState);
+                  markRepoNotificationsDone(repoNotifications[0]);
+                }}
+              />
+            )}
             <InteractionButton
               title="Mark Repository as Read"
               icon={ReadIcon}
diff --git a/src/components/settings/NotificationSettings.tsx b/src/components/settings/NotificationSettings.tsx
index f9fac93e5..1a7096285 100644
--- a/src/components/settings/NotificationSettings.tsx
+++ b/src/components/settings/NotificationSettings.tsx
@@ -56,6 +56,12 @@ export const NotificationSettings: FC = () => {
         onChange={(evt) =>
           updateSetting('markAsDoneOnOpen', evt.target.checked)
         }
+        tooltip={
+          <div>
+            <strong>Mark as Done</strong> feature is supported in GitHub Cloud
+            and GitHub Enterprise Server 3.13 or later.
+          </div>
+        }
       />
       <Checkbox
         name="delayNotificationState"
diff --git a/src/context/App.tsx b/src/context/App.tsx
index 90cf29a1d..67857be5e 100644
--- a/src/context/App.tsx
+++ b/src/context/App.tsx
@@ -262,6 +262,13 @@ export const AppProvider = ({ children }: { children: ReactNode }) => {
       );
       return existing.settings;
     }
+
+    for (const account of auth.accounts.filter(
+      (a) => a.platform === 'GitHub Enterprise Server',
+    )) {
+      const res = await headNotifications(account.hostname, account.token);
+      account.version = res.headers['x-github-enterprise-version'];
+    }
   }, []);
 
   const fetchNotificationsWithAccounts = useCallback(
diff --git a/src/hooks/useNotifications.ts b/src/hooks/useNotifications.ts
index 76415d384..a5f385ab2 100644
--- a/src/hooks/useNotifications.ts
+++ b/src/hooks/useNotifications.ts
@@ -13,6 +13,7 @@ import {
   markRepositoryNotificationsAsRead,
 } from '../utils/api/client';
 import { getAccountUUID } from '../utils/auth/utils';
+import { isMarkAsDoneFeatureSupported } from '../utils/helpers';
 import {
   getAllNotifications,
   setTrayIconColor,
@@ -120,11 +121,13 @@ export const useNotifications = (): NotificationsState => {
       setStatus('loading');
 
       try {
-        await markNotificationThreadAsDone(
-          notification.id,
-          notification.account.hostname,
-          notification.account.token,
-        );
+        if (isMarkAsDoneFeatureSupported(notification.account)) {
+          await markNotificationThreadAsDone(
+            notification.id,
+            notification.account.hostname,
+            notification.account.token,
+          );
+        }
 
         const updatedNotifications = removeNotification(
           state.settings,
diff --git a/src/routes/__snapshots__/Settings.test.tsx.snap b/src/routes/__snapshots__/Settings.test.tsx.snap
index e5b4f9869..54e98764e 100644
--- a/src/routes/__snapshots__/Settings.test.tsx.snap
+++ b/src/routes/__snapshots__/Settings.test.tsx.snap
@@ -486,6 +486,26 @@ exports[`routes/Settings.tsx should render itself & its children 1`] = `
               for="markAsDoneOnOpen"
             >
               Mark as done on open
+              <span
+                aria-label="tooltip-markAsDoneOnOpen"
+                class="relative"
+                id="tooltip-markAsDoneOnOpen"
+              >
+                <svg
+                  aria-hidden="true"
+                  class="ml-1 text-blue-500"
+                  fill="currentColor"
+                  focusable="false"
+                  height="16"
+                  style="display: inline-block; user-select: none; vertical-align: text-bottom; overflow: visible;"
+                  viewBox="0 0 16 16"
+                  width="16"
+                >
+                  <path
+                    d="M0 8a8 8 0 1 1 16 0A8 8 0 0 1 0 8Zm8-6.5a6.5 6.5 0 1 0 0 13 6.5 6.5 0 0 0 0-13ZM6.92 6.085h.001a.749.749 0 1 1-1.342-.67c.169-.339.436-.701.849-.977C6.845 4.16 7.369 4 8 4a2.756 2.756 0 0 1 1.637.525c.503.377.863.965.863 1.725 0 .448-.115.83-.329 1.15-.205.307-.47.513-.692.662-.109.072-.22.138-.313.195l-.006.004a6.24 6.24 0 0 0-.26.16.952.952 0 0 0-.276.245.75.75 0 0 1-1.248-.832c.184-.264.42-.489.692-.661.103-.067.207-.132.313-.195l.007-.004c.1-.061.182-.11.258-.161a.969.969 0 0 0 .277-.245C8.96 6.514 9 6.427 9 6.25a.612.612 0 0 0-.262-.525A1.27 1.27 0 0 0 8 5.5c-.369 0-.595.09-.74.187a1.01 1.01 0 0 0-.34.398ZM9 11a1 1 0 1 1-2 0 1 1 0 0 1 2 0Z"
+                  />
+                </svg>
+              </span>
             </label>
           </div>
         </div>
diff --git a/src/types.ts b/src/types.ts
index e7cac771f..09ac84a8b 100644
--- a/src/types.ts
+++ b/src/types.ts
@@ -46,6 +46,7 @@ export type Status = 'loading' | 'success' | 'error';
 export interface Account {
   method: AuthMethod;
   platform: PlatformType;
+  version?: string;
   hostname: Hostname;
   token: Token;
   user: GitifyUser | null;
diff --git a/src/utils/api/__snapshots__/client.test.ts.snap b/src/utils/api/__snapshots__/client.test.ts.snap
index 7f0db3198..dc98f15e5 100644
--- a/src/utils/api/__snapshots__/client.test.ts.snap
+++ b/src/utils/api/__snapshots__/client.test.ts.snap
@@ -36,7 +36,7 @@ exports[`utils/api/client.ts headNotifications should fetch notifications head -
 }
 `;
 
-exports[`utils/api/client.ts ignoreNotificationThreadSubscription should ignore notification thread subscription - github 1`] = `
+exports[`utils/api/client.ts ignoreNotificationThreadSubscription should ignore notification thread subscription - enterprise 1`] = `
 {
   "Accept": "application/json",
   "Authorization": "token token-123-456",
@@ -45,7 +45,7 @@ exports[`utils/api/client.ts ignoreNotificationThreadSubscription should ignore
 }
 `;
 
-exports[`utils/api/client.ts ignoreNotificationThreadSubscription should ignore notification thread subscription- enterprise 1`] = `
+exports[`utils/api/client.ts ignoreNotificationThreadSubscription should ignore notification thread subscription - github 1`] = `
 {
   "Accept": "application/json",
   "Authorization": "token token-123-456",
@@ -72,7 +72,7 @@ exports[`utils/api/client.ts listNotificationsForAuthenticatedUser should list n
 }
 `;
 
-exports[`utils/api/client.ts markNotificationThreadAsDone should mark notification thread as done - github 1`] = `
+exports[`utils/api/client.ts markNotificationThreadAsDone should mark notification thread as done - enterprise 1`] = `
 {
   "Accept": "application/json",
   "Authorization": "token token-123-456",
@@ -81,7 +81,7 @@ exports[`utils/api/client.ts markNotificationThreadAsDone should mark notificati
 }
 `;
 
-exports[`utils/api/client.ts markNotificationThreadAsDone should mark notification thread as done- enterprise 1`] = `
+exports[`utils/api/client.ts markNotificationThreadAsDone should mark notification thread as done - github 1`] = `
 {
   "Accept": "application/json",
   "Authorization": "token token-123-456",
@@ -90,7 +90,7 @@ exports[`utils/api/client.ts markNotificationThreadAsDone should mark notificati
 }
 `;
 
-exports[`utils/api/client.ts markNotificationThreadAsRead should mark notification thread as read - github 1`] = `
+exports[`utils/api/client.ts markNotificationThreadAsRead should mark notification thread as read - enterprise 1`] = `
 {
   "Accept": "application/json",
   "Authorization": "token token-123-456",
@@ -99,7 +99,7 @@ exports[`utils/api/client.ts markNotificationThreadAsRead should mark notificati
 }
 `;
 
-exports[`utils/api/client.ts markNotificationThreadAsRead should mark notification thread as read- enterprise 1`] = `
+exports[`utils/api/client.ts markNotificationThreadAsRead should mark notification thread as read - github 1`] = `
 {
   "Accept": "application/json",
   "Authorization": "token token-123-456",
diff --git a/src/utils/api/client.test.ts b/src/utils/api/client.test.ts
index 614758c16..edf0b0325 100644
--- a/src/utils/api/client.test.ts
+++ b/src/utils/api/client.test.ts
@@ -135,7 +135,7 @@ describe('utils/api/client.ts', () => {
       expect(axios.defaults.headers.common).toMatchSnapshot();
     });
 
-    it('should mark notification thread as read- enterprise', async () => {
+    it('should mark notification thread as read - enterprise', async () => {
       await markNotificationThreadAsRead(
         mockThreadId,
         mockEnterpriseHostname,
@@ -169,7 +169,7 @@ describe('utils/api/client.ts', () => {
       expect(axios.defaults.headers.common).toMatchSnapshot();
     });
 
-    it('should mark notification thread as done- enterprise', async () => {
+    it('should mark notification thread as done - enterprise', async () => {
       await markNotificationThreadAsDone(
         mockThreadId,
         mockEnterpriseHostname,
@@ -203,7 +203,7 @@ describe('utils/api/client.ts', () => {
       expect(axios.defaults.headers.common).toMatchSnapshot();
     });
 
-    it('should ignore notification thread subscription- enterprise', async () => {
+    it('should ignore notification thread subscription - enterprise', async () => {
       await ignoreNotificationThreadSubscription(
         mockThreadId,
         mockEnterpriseHostname,
diff --git a/src/utils/api/client.ts b/src/utils/api/client.ts
index c558b24bb..d3b358376 100644
--- a/src/utils/api/client.ts
+++ b/src/utils/api/client.ts
@@ -90,6 +90,8 @@ export function markNotificationThreadAsRead(
  * Marks a thread as "done." Marking a thread as "done" is equivalent to marking a
  * notification in your notification inbox on GitHub as done.
  *
+ * NOTE: This was added to GitHub Enterprise Server in version 3.13 or later.
+ *
  * Endpoint documentation: https://docs.github.com/en/rest/activity/notifications#mark-a-thread-as-done
  */
 export function markNotificationThreadAsDone(
@@ -99,7 +101,6 @@ export function markNotificationThreadAsDone(
 ): AxiosPromise<void> {
   const url = getGitHubAPIBaseUrl(hostname);
   url.pathname += `notifications/threads/${threadId}`;
-
   return apiRequestAuth(url.toString() as Link, 'DELETE', token, {});
 }
 
diff --git a/src/utils/helpers.test.ts b/src/utils/helpers.test.ts
index 805c740b4..0cdbc7b72 100644
--- a/src/utils/helpers.test.ts
+++ b/src/utils/helpers.test.ts
@@ -1,5 +1,9 @@
 import type { AxiosPromise, AxiosResponse } from 'axios';
-import { mockPersonalAccessTokenAccount } from '../__mocks__/state-mocks';
+import {
+  mockGitHubCloudAccount,
+  mockGitHubEnterpriseServerAccount,
+  mockPersonalAccessTokenAccount,
+} from '../__mocks__/state-mocks';
 
 import { defaultSettings } from '../context/App';
 import type { Hostname, Link, SettingsState } from '../types';
@@ -17,6 +21,7 @@ import {
   getFilterCount,
   getPlatformFromHostname,
   isEnterpriseServerHost,
+  isMarkAsDoneFeatureSupported,
 } from './helpers';
 
 describe('utils/helpers.ts', () => {
@@ -56,6 +61,48 @@ describe('utils/helpers.ts', () => {
     });
   });
 
+  describe('isMarkAsDoneFeatureSupported', () => {
+    it('should return true for GitHub Cloud', () => {
+      expect(isMarkAsDoneFeatureSupported(mockGitHubCloudAccount)).toBe(true);
+    });
+
+    it('should return false for GitHub Enterprise Server < v3.13', () => {
+      const account = {
+        ...mockGitHubEnterpriseServerAccount,
+        version: '3.12.0',
+      };
+
+      expect(isMarkAsDoneFeatureSupported(account)).toBe(false);
+    });
+
+    it('should return true for GitHub Enterprise Server >= v3.13', () => {
+      const account = {
+        ...mockGitHubEnterpriseServerAccount,
+        version: '3.13.3',
+      };
+
+      expect(isMarkAsDoneFeatureSupported(account)).toBe(true);
+    });
+
+    it('should return false for GitHub Enterprise Server when partial version available', () => {
+      const account = {
+        ...mockGitHubEnterpriseServerAccount,
+        version: '3',
+      };
+
+      expect(isMarkAsDoneFeatureSupported(account)).toBe(false);
+    });
+
+    it('should return false for GitHub Enterprise Server when no version available', () => {
+      const account = {
+        ...mockGitHubEnterpriseServerAccount,
+        version: null,
+      };
+
+      expect(isMarkAsDoneFeatureSupported(account)).toBe(false);
+    });
+  });
+
   describe('generateNotificationReferrerId', () => {
     it('should generate the notification_referrer_id', () => {
       const referrerId = generateNotificationReferrerId(mockSingleNotification);
diff --git a/src/utils/helpers.ts b/src/utils/helpers.ts
index a0724bfe3..10094b417 100644
--- a/src/utils/helpers.ts
+++ b/src/utils/helpers.ts
@@ -1,6 +1,6 @@
 import { formatDistanceToNowStrict, parseISO } from 'date-fns';
 import { defaultSettings } from '../context/App';
-import type { Hostname, Link, SettingsState } from '../types';
+import type { Account, Hostname, Link, SettingsState } from '../types';
 import type { Notification } from '../typesGitHub';
 import { getHtmlUrl, getLatestDiscussion } from './api/client';
 import type { PlatformType } from './auth/types';
@@ -21,6 +21,20 @@ export function isEnterpriseServerHost(hostname: Hostname): boolean {
   return !hostname.endsWith(Constants.DEFAULT_AUTH_OPTIONS.hostname);
 }
 
+export function isMarkAsDoneFeatureSupported(account: Account): boolean {
+  if (isEnterpriseServerHost(account.hostname)) {
+    // Support for "Mark as Done" was added to GitHub Enterprise Server in v3.13 or newer
+    if (account.version) {
+      const version = account?.version.split('.').map(Number);
+      return version[0] >= 3 && version[1] >= 13;
+    }
+
+    return false;
+  }
+
+  return true;
+}
+
 export function generateNotificationReferrerId(
   notification: Notification,
 ): string {