diff --git a/lib/rbs/cli.rb b/lib/rbs/cli.rb
index bb32fe430..956e47a54 100644
--- a/lib/rbs/cli.rb
+++ b/lib/rbs/cli.rb
@@ -1248,7 +1248,11 @@ def run_subtract(args, _)
           w.write(subtracted)
 
           if write_to_file
-            rbs_path.write(io.string)
+            if io.string.empty?
+              rbs_path.delete
+            else
+              rbs_path.write(io.string)
+            end
           else
             stdout.puts(io.string)
           end
diff --git a/test/rbs/cli_test.rb b/test/rbs/cli_test.rb
index 2c28a4f52..7bb1fe02c 100644
--- a/test/rbs/cli_test.rb
+++ b/test/rbs/cli_test.rb
@@ -966,6 +966,31 @@ def y: () -> untyped
     end
   end
 
+
+  def test_subtract_write_removes_definition_if_empty
+    Dir.mktmpdir do |dir|
+      dir = Pathname(dir)
+
+      minuend = dir.join('minuend.rbs')
+      minuend.write(<<~RBS)
+        class C
+          def x: () -> untyped
+        end
+      RBS
+      subtrahend = dir.join('subtrahend.rbs')
+      subtrahend.write(<<~RBS)
+        class C
+          def x: () -> untyped
+        end
+      RBS
+
+      stdout, stderr = run_rbs('subtract', '--write', minuend.to_s, subtrahend.to_s)
+      assert_empty stderr
+      assert_empty stdout
+      assert_equal minuend.exist?, false
+    end
+  end
+
   def assert_rbs_test_no_errors cli, dir, arg_array
     args = ['-I', dir.to_s, 'test', *arg_array]
     assert_instance_of Process::Status, cli.run(args)