diff --git a/packages/core/src/services/fileDiscoveryService.test.ts b/packages/core/src/services/fileDiscoveryService.test.ts
index c205463bc2..63ddc06616 100644
--- a/packages/core/src/services/fileDiscoveryService.test.ts
+++ b/packages/core/src/services/fileDiscoveryService.test.ts
@@ -502,6 +502,50 @@ describe('FileDiscoveryService', () => {
       const paths = service.getAllIgnoreFilePaths();
       expect(paths[0]).toBe(path.join(projectRoot, '.gitignore'));
     });
+
+    it('should exclude directories from getIgnoreFilePaths (#19868)', async () => {
+      // Create a directory that shares a name with a customIgnoreFilePaths entry
+      await fs.mkdir(path.join(projectRoot, 'node_modules'), {
+        recursive: true,
+      });
+
+      const service = new FileDiscoveryService(projectRoot, {
+        customIgnoreFilePaths: ['node_modules'],
+      });
+      const paths = service.getIgnoreFilePaths();
+
+      // node_modules/ is a directory, not a file — it should be excluded
+      expect(paths).not.toContain(path.join(projectRoot, 'node_modules'));
+    });
+
+    it('should exclude directories from getAllIgnoreFilePaths (#19868)', async () => {
+      await fs.mkdir(path.join(projectRoot, 'node_modules'), {
+        recursive: true,
+      });
+
+      const service = new FileDiscoveryService(projectRoot, {
+        customIgnoreFilePaths: ['node_modules'],
+      });
+      const paths = service.getAllIgnoreFilePaths();
+
+      expect(paths).not.toContain(path.join(projectRoot, 'node_modules'));
+      // .gitignore should still be present
+      expect(paths).toContain(path.join(projectRoot, '.gitignore'));
+    });
+
+    it('should not crash when customIgnoreFilePaths contains directory names (#19868)', async () => {
+      await fs.mkdir(path.join(projectRoot, 'node_modules'), {
+        recursive: true,
+      });
+      await fs.mkdir(path.join(projectRoot, 'temp'), { recursive: true });
+
+      // This is the exact user scenario from issue #19868
+      expect(() => {
+        new FileDiscoveryService(projectRoot, {
+          customIgnoreFilePaths: ['node_modules/', 'temp/', 'cache/'],
+        });
+      }).not.toThrow();
+    });
   });
 
   describe('getIgnoredPaths', () => {
diff --git a/packages/core/src/services/fileDiscoveryService.ts b/packages/core/src/services/fileDiscoveryService.ts
index 28b55894b6..d58f31a749 100644
--- a/packages/core/src/services/fileDiscoveryService.ts
+++ b/packages/core/src/services/fileDiscoveryService.ts
@@ -274,7 +274,8 @@ export class FileDiscoveryService {
       this.defaultFilterFileOptions.respectGitIgnore
     ) {
       const gitIgnorePath = path.join(this.projectRoot, '.gitignore');
-      if (fs.existsSync(gitIgnorePath)) {
+      const stat = fs.statSync(gitIgnorePath, { throwIfNoEntry: false });
+      if (stat?.isFile()) {
         paths.push(gitIgnorePath);
       }
     }
diff --git a/packages/core/src/utils/filesearch/ignore.ts b/packages/core/src/utils/filesearch/ignore.ts
index b8b2635c19..bd5cd5d6e9 100644
--- a/packages/core/src/utils/filesearch/ignore.ts
+++ b/packages/core/src/utils/filesearch/ignore.ts
@@ -19,8 +19,10 @@ export function loadIgnoreRules(
   const ignoreFiles = service.getAllIgnoreFilePaths();
 
   for (const filePath of ignoreFiles) {
-    if (fs.existsSync(filePath)) {
+    try {
       ignorer.add(fs.readFileSync(filePath, 'utf8'));
+    } catch {
+      // Skip files that can't be read (e.g. directories, permission errors)
     }
   }
 
diff --git a/packages/core/src/utils/ignoreFileParser.ts b/packages/core/src/utils/ignoreFileParser.ts
index 991826e3f0..ee7284bfa6 100644
--- a/packages/core/src/utils/ignoreFileParser.ts
+++ b/packages/core/src/utils/ignoreFileParser.ts
@@ -105,7 +105,10 @@ export class IgnoreFileParser implements IgnoreFileFilter {
       .slice()
       .reverse()
       .map((fileName) => path.join(this.projectRoot, fileName))
-      .filter((filePath) => fs.existsSync(filePath));
+      .filter(
+        (filePath) =>
+          fs.statSync(filePath, { throwIfNoEntry: false })?.isFile() ?? false,
+      );
   }
 
   /**