diff --git a/docs/changelog/126385.yaml b/docs/changelog/126385.yaml
new file mode 100644
index 000000000000..c59d1f15c6ea
--- /dev/null
+++ b/docs/changelog/126385.yaml
@@ -0,0 +1,6 @@
+pr: 126385
+summary: Filter out empty top docs results before merging
+area: Search
+type: bug
+issues:
+ - 126118
diff --git a/server/src/main/java/org/elasticsearch/action/search/SearchPhaseController.java b/server/src/main/java/org/elasticsearch/action/search/SearchPhaseController.java
index e2bb32466472..4f028bfb8576 100644
--- a/server/src/main/java/org/elasticsearch/action/search/SearchPhaseController.java
+++ b/server/src/main/java/org/elasticsearch/action/search/SearchPhaseController.java
@@ -150,11 +150,11 @@ public final class SearchPhaseController {
             return topDocs;
         } else if (topDocs instanceof TopFieldGroups firstTopDocs) {
             final Sort sort = new Sort(firstTopDocs.fields);
-            final TopFieldGroups[] shardTopDocs = results.toArray(new TopFieldGroups[0]);
+            final TopFieldGroups[] shardTopDocs = results.stream().filter(td -> td != Lucene.EMPTY_TOP_DOCS).toArray(TopFieldGroups[]::new);
             mergedTopDocs = TopFieldGroups.merge(sort, from, topN, shardTopDocs, false);
         } else if (topDocs instanceof TopFieldDocs firstTopDocs) {
             final Sort sort = checkSameSortTypes(results, firstTopDocs.fields);
-            final TopFieldDocs[] shardTopDocs = results.toArray(new TopFieldDocs[0]);
+            final TopFieldDocs[] shardTopDocs = results.stream().filter((td -> td != Lucene.EMPTY_TOP_DOCS)).toArray(TopFieldDocs[]::new);
             mergedTopDocs = TopDocs.merge(sort, from, topN, shardTopDocs);
         } else {
             final TopDocs[] shardTopDocs = results.toArray(new TopDocs[numShards]);