diff --git a/cmd/nonmem.go b/cmd/nonmem.go
index 72735caf..1a857f34 100644
--- a/cmd/nonmem.go
+++ b/cmd/nonmem.go
@@ -512,6 +512,13 @@ func filesToCleanup(model *NonMemModel, exceptions ...string) runner.FileCleanIn
 				}
 			}
 		}
+
+		re_wk := regexp.MustCompile("^WK_[0-9]+")
+		for _, f := range files {
+			if f.Size() == 0 && !f.IsDir() && re_wk.MatchString(f.Name()) {
+				fci.FilesToRemove = append(fci.FilesToRemove, newTargetFile(f.Name(), model.Configuration.CleanLvl))
+			}
+		}
 	}
 
 	return fci
diff --git a/integration/nonmem.go b/integration/nonmem.go
index 411fa5ac..cd9b8cb3 100644
--- a/integration/nonmem.go
+++ b/integration/nonmem.go
@@ -60,6 +60,13 @@ func AssertNonMemCleanedUpFiles(t *wrapt.T, details NonMemTestingDetails) {
 			t.A.NoFileExists(filepath.Join(details.OutputDir, f))
 		}
 	}
+
+	// Parallelization-related files handled by nonmem.filesToCleanup().
+	files, err := os.ReadDir(details.OutputDir)
+	t.R.NoError(err)
+	for _, fi := range files {
+		t.R.NotRegexp("^WK_", fi.Name())
+	}
 }
 
 func AssertBBIConfigJSONCreated(t *wrapt.T, details NonMemTestingDetails) {