diff --git a/CHANGELOG.md b/CHANGELOG.md
index 045f045f0b..020c9b16c7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -46,6 +46,7 @@ We use *breaking :warning:* to mark changes that are not backward compatible (re
 - [#6325](https://github.com/thanos-io/thanos/pull/6325) Store: return gRPC resource exhausted error for byte limiter.
 - [#6399](https://github.com/thanos-io/thanos/pull/6399) *: Fix double-counting bug in http_request_duration metric
 - [#6428](https://github.com/thanos-io/thanos/pull/6428) Report gRPC connnection errors in the logs.
+- [#6519](https://github.com/thanos-io/thanos/pull/6519) Reloader: Use timeout for initial apply.
 - [#6509](https://github.com/thanos-io/thanos/pull/6509) Store Gateway: Remove `memWriter` from `fileWriter` to reduce memory usage when sync index headers.
 
 ### Changed
diff --git a/pkg/reloader/reloader.go b/pkg/reloader/reloader.go
index 1072026c2a..2057ea5f75 100644
--- a/pkg/reloader/reloader.go
+++ b/pkg/reloader/reloader.go
@@ -207,8 +207,10 @@ func (r *Reloader) Watch(ctx context.Context) error {
 		if err := r.watcher.addFile(r.cfgFile); err != nil {
 			return errors.Wrapf(err, "add config file %s to watcher", r.cfgFile)
 		}
-
-		if err := r.apply(ctx); err != nil {
+		initialSyncCtx, initialSyncCancel := context.WithTimeout(ctx, r.watchInterval)
+		err := r.apply(initialSyncCtx)
+		initialSyncCancel()
+		if err != nil {
 			return err
 		}
 	}