diff --git a/.changeset/orange-beans-float.md b/.changeset/orange-beans-float.md
new file mode 100644
index 0000000000..7e31277890
--- /dev/null
+++ b/.changeset/orange-beans-float.md
@@ -0,0 +1,5 @@
+---
+'@backstage/plugin-catalog-backend-module-github': patch
+---
+
+Fix bug in root repo import where catalog-info.yaml.hcl file is found by search and breaks the import
diff --git a/plugins/catalog-backend-module-github/src/analyzers/GithubLocationAnalyzer.test.ts b/plugins/catalog-backend-module-github/src/analyzers/GithubLocationAnalyzer.test.ts
index b745dd37ba..e5c7eb5896 100644
--- a/plugins/catalog-backend-module-github/src/analyzers/GithubLocationAnalyzer.test.ts
+++ b/plugins/catalog-backend-module-github/src/analyzers/GithubLocationAnalyzer.test.ts
@@ -112,7 +112,7 @@ describe('GithubLocationAnalyzer', () => {
 
   it('should analyze', async () => {
     octokit.search.code.mockImplementation((opts: { q: string }) => {
-      if (opts.q === 'filename:catalog-info.yaml repo:foo/bar') {
+      if (opts.q === 'filename:catalog-info.yaml extension:yaml repo:foo/bar') {
         return Promise.resolve({
           data: { items: [{ path: 'catalog-info.yaml' }], total_count: 1 },
         });
@@ -139,7 +139,7 @@ describe('GithubLocationAnalyzer', () => {
 
   it('should use the provided entity filename for search', async () => {
     octokit.search.code.mockImplementation((opts: { q: string }) => {
-      if (opts.q === 'filename:anvil.yaml repo:foo/bar') {
+      if (opts.q === 'filename:anvil.yaml extension:yaml repo:foo/bar') {
         return Promise.resolve({
           data: { items: [{ path: 'anvil.yaml' }], total_count: 1 },
         });
@@ -162,4 +162,30 @@ describe('GithubLocationAnalyzer', () => {
       target: 'https://github.com/foo/bar/blob/my_default_branch/anvil.yaml',
     });
   });
+
+  it('should use the provided entity file extension in search query only if present', async () => {
+    octokit.search.code.mockImplementation((opts: { q: string }) => {
+      if (opts.q === 'filename:.gitignore  repo:foo/bar') {
+        return Promise.resolve({
+          data: { items: [{ path: '.gitignore' }], total_count: 1 },
+        });
+      }
+      return Promise.reject();
+    });
+
+    const analyzer = new GithubLocationAnalyzer({
+      discovery: mockDiscoveryApi,
+      auth: mockAuthService,
+      config,
+    });
+    const result = await analyzer.analyze({
+      url: 'https://github.com/foo/bar',
+      catalogFilename: '.gitignore',
+    });
+
+    expect(result.existing[0].location).toEqual({
+      type: 'url',
+      target: 'https://github.com/foo/bar/blob/my_default_branch/.gitignore',
+    });
+  });
 });
diff --git a/plugins/catalog-backend-module-github/src/analyzers/GithubLocationAnalyzer.ts b/plugins/catalog-backend-module-github/src/analyzers/GithubLocationAnalyzer.ts
index 2648b1bcdc..7e6ac73054 100644
--- a/plugins/catalog-backend-module-github/src/analyzers/GithubLocationAnalyzer.ts
+++ b/plugins/catalog-backend-module-github/src/analyzers/GithubLocationAnalyzer.ts
@@ -22,7 +22,7 @@ import {
   ScmIntegrations,
 } from '@backstage/integration';
 import { Octokit } from '@octokit/rest';
-import { trimEnd } from 'lodash';
+import { isEmpty, trimEnd } from 'lodash';
 import parseGitUrl from 'git-url-parse';
 import {
   AnalyzeOptions,
@@ -35,6 +35,7 @@ import {
 } from '@backstage/backend-common';
 import { Config } from '@backstage/config';
 import { AuthService } from '@backstage/backend-plugin-api';
+import { extname } from 'path';
 
 /** @public */
 export type GithubLocationAnalyzerOptions = {
@@ -76,8 +77,12 @@ export class GithubLocationAnalyzer implements ScmLocationAnalyzer {
     const { owner, name: repo } = parseGitUrl(url);
 
     const catalogFile = catalogFilename || 'catalog-info.yaml';
+    const extension = extname(catalogFile);
+    const extensionQuery = !isEmpty(extension)
+      ? `extension:${extension.replace('.', '')}`
+      : '';
 
-    const query = `filename:${catalogFile} repo:${owner}/${repo}`;
+    const query = `filename:${catalogFile} ${extensionQuery} repo:${owner}/${repo}`;
 
     const integration = this.integrations.github.byUrl(url);
     if (!integration) {