diff --git a/packages/vite/src/node/plugins/importAnalysis.ts b/packages/vite/src/node/plugins/importAnalysis.ts
index d26b0e219085d9..868207bf2ae2c8 100644
--- a/packages/vite/src/node/plugins/importAnalysis.ts
+++ b/packages/vite/src/node/plugins/importAnalysis.ts
@@ -478,7 +478,9 @@ export function importAnalysisPlugin(config: ResolvedConfig): Plugin {
           const [url, resolvedId] = await normalizeUrl(specifier, start)
 
           // record as safe modules
-          server?.moduleGraph.safeModulesPath.add(fsPathFromUrl(url))
+          const urlWithoutBase =
+            base !== '/' && url.startsWith(base) ? url.replace(base, '/') : url
+          server?.moduleGraph.safeModulesPath.add(fsPathFromUrl(urlWithoutBase))
 
           if (url !== specifier) {
             let rewriteDone = false