diff --git a/CHANGELOG.md b/CHANGELOG.md
index fb80ecf0f..76dcd736d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -11,6 +11,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Bumped AI SDK and associated packages version. [#752](https://github.com/sourcebot-dev/sourcebot/pull/752)
 - Bumped Node.js version to v24. [#753](https://github.com/sourcebot-dev/sourcebot/pull/753)
 
+### Fixed
+- Fixed "Repository not found for file: x" error when searching in orphaned shards. [#761](https://github.com/sourcebot-dev/sourcebot/pull/761)
+
 ## [4.10.12] - 2026-01-16
 
 ### Changed
diff --git a/packages/web/src/features/search/zoektSearcher.ts b/packages/web/src/features/search/zoektSearcher.ts
index 5bdea8bce..61cefdcf1 100644
--- a/packages/web/src/features/search/zoektSearcher.ts
+++ b/packages/web/src/features/search/zoektSearcher.ts
@@ -17,6 +17,7 @@ import { createLogger, env } from "@sourcebot/shared";
 import path from 'path';
 import { isBranchQuery, QueryIR, someInQueryIR } from './ir';
 import { RepositoryInfo, SearchResponse, SearchResultFile, SearchStats, SourceRange, StreamedSearchErrorResponse, StreamedSearchResponse } from "./types";
+import { captureEvent } from "@/lib/posthog";
 
 const logger = createLogger("zoekt-searcher");
 
@@ -383,9 +384,17 @@ const transformZoektSearchResponse = async (response: ZoektGrpcSearchResponse, r
         const repoId = getRepoIdForFile(file);
         const repo = reposMapCache.get(repoId);
 
-        // This should never happen.
+        // This can happen when a shard exists for a repository that does not exist in the database.
+        // In this case, issue a error message and skip the file.
+        // @see: https://github.com/sourcebot-dev/sourcebot/issues/669
         if (!repo) {
-            throw new Error(`Repository not found for file: ${file.file_name}`);
+            const errorMessage = `Unable to find repository "${file.repository}" in database for file "${file.file_name}". This can happen when a search shard exists for a repository that does not exist in the database. See https://github.com/sourcebot-dev/sourcebot/issues/669 for more details. Skipping file...`;
+
+            logger.error(errorMessage);
+            Sentry.captureMessage(errorMessage);
+            captureEvent('wa_repo_not_found_for_zoekt_file', {});
+
+            return undefined;
         }
 
         // @todo: address "file_name might not be a valid UTF-8 string" warning.
diff --git a/packages/web/src/lib/posthogEvents.ts b/packages/web/src/lib/posthogEvents.ts
index 36df22a71..eee32bc05 100644
--- a/packages/web/src/lib/posthogEvents.ts
+++ b/packages/web/src/lib/posthogEvents.ts
@@ -185,6 +185,8 @@ export type PosthogEventMap = {
         durationMs: number,
     },
     //////////////////////////////////////////////////////////////////
+    wa_repo_not_found_for_zoekt_file: {},
+    //////////////////////////////////////////////////////////////////
     api_code_search_request: {
         source: string;
         type: 'streamed' | 'blocking';