diff --git a/docs/changelog/88946.yaml b/docs/changelog/88946.yaml
new file mode 100644
index 000000000000..ae853f2e5ffa
--- /dev/null
+++ b/docs/changelog/88946.yaml
@@ -0,0 +1,6 @@
+pr: 88946
+summary: "Graph: fix race condition in timeout"
+area: Graph
+type: bug
+issues:
+ - 55396
diff --git a/x-pack/plugin/graph/src/internalClusterTest/java/org/elasticsearch/xpack/graph/test/GraphTests.java b/x-pack/plugin/graph/src/internalClusterTest/java/org/elasticsearch/xpack/graph/test/GraphTests.java
index 7623fffa777f..e9178675bd1a 100644
--- a/x-pack/plugin/graph/src/internalClusterTest/java/org/elasticsearch/xpack/graph/test/GraphTests.java
+++ b/x-pack/plugin/graph/src/internalClusterTest/java/org/elasticsearch/xpack/graph/test/GraphTests.java
@@ -222,19 +222,18 @@ public class GraphTests extends ESSingleNodeTestCase {
         assertNull("Elvis is a 3rd tier connection so should not be returned here", response.getVertex(Vertex.createId("people", "elvis")));
     }
 
-    @AwaitsFix(bugUrl = "https://github.com/elastic/elasticsearch/issues/55396")
     public void testTimedoutQueryCrawl() {
         GraphExploreRequestBuilder grb = new GraphExploreRequestBuilder(client(), GraphExploreAction.INSTANCE).setIndices("test");
         grb.setTimeout(TimeValue.timeValueMillis(400));
         Hop hop1 = grb.createNextHop(QueryBuilders.termQuery("description", "beatles"));
         hop1.addVertexRequest("people").size(10).minDocCount(1); // members of beatles
-        // 00s friends of beatles
-        grb.createNextHop(QueryBuilders.termQuery("decade", "00s")).addVertexRequest("people").size(100).minDocCount(1);
         // A query that should cause a timeout
         ScriptQueryBuilder timeoutQuery = QueryBuilders.scriptQuery(
             new Script(ScriptType.INLINE, "mockscript", "graph_timeout", Collections.emptyMap())
         );
         grb.createNextHop(timeoutQuery).addVertexRequest("people").size(100).minDocCount(1);
+        // 00s friends of beatles
+        grb.createNextHop(QueryBuilders.termQuery("decade", "00s")).addVertexRequest("people").size(100).minDocCount(1);
 
         GraphExploreResponse response = grb.get();
         assertTrue(response.isTimedOut());
diff --git a/x-pack/plugin/graph/src/main/java/org/elasticsearch/xpack/graph/action/TransportGraphExploreAction.java b/x-pack/plugin/graph/src/main/java/org/elasticsearch/xpack/graph/action/TransportGraphExploreAction.java
index b50cd54bbbe4..93c28f63b0e8 100644
--- a/x-pack/plugin/graph/src/main/java/org/elasticsearch/xpack/graph/action/TransportGraphExploreAction.java
+++ b/x-pack/plugin/graph/src/main/java/org/elasticsearch/xpack/graph/action/TransportGraphExploreAction.java
@@ -6,6 +6,8 @@
  */
 package org.elasticsearch.xpack.graph.action;
 
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.apache.lucene.search.BooleanQuery;
 import org.apache.lucene.util.BytesRef;
 import org.apache.lucene.util.PriorityQueue;
@@ -61,13 +63,13 @@ import java.util.Map.Entry;
 import java.util.Set;
 import java.util.SortedSet;
 import java.util.TreeSet;
-import java.util.concurrent.atomic.AtomicBoolean;
 
 /**
  * Performs a series of elasticsearch queries and aggregations to explore
  * connected terms in a single index.
  */
 public class TransportGraphExploreAction extends HandledTransportAction<GraphExploreRequest, GraphExploreResponse> {
+    private static final Logger logger = LogManager.getLogger(TransportGraphExploreAction.class);
 
     private final ThreadPool threadPool;
     private final NodeClient client;
@@ -115,7 +117,6 @@ public class TransportGraphExploreAction extends HandledTransportAction<GraphExp
         private final ActionListener<GraphExploreResponse> listener;
 
         private final long startTime;
-        private final AtomicBoolean timedOut;
         private volatile ShardOperationFailedException[] shardFailures;
         private Map<VertexId, Vertex> vertices = new HashMap<>();
         private Map<ConnectionId, Connection> connections = new HashMap<>();
@@ -128,7 +129,6 @@ public class TransportGraphExploreAction extends HandledTransportAction<GraphExp
             this.request = request;
             this.listener = listener;
             this.startTime = threadPool.relativeTimeInMillis();
-            this.timedOut = new AtomicBoolean(false);
             this.shardFailures = ShardSearchFailure.EMPTY_ARRAY;
         }
 
@@ -173,16 +173,11 @@ public class TransportGraphExploreAction extends HandledTransportAction<GraphExp
          * connections
          */
         synchronized void expand() {
-            if (hasTimedOut()) {
-                timedOut.set(true);
-                listener.onResponse(buildResponse());
-                return;
-            }
             Map<String, Set<Vertex>> lastHopFindings = hopFindings.get(currentHopNumber);
             if ((currentHopNumber >= (request.getHopNumbers() - 1)) || (lastHopFindings == null) || (lastHopFindings.size() == 0)) {
                 // Either we gathered no leads from the last hop or we have
                 // reached the final hop
-                listener.onResponse(buildResponse());
+                listener.onResponse(buildResponse(false));
                 return;
             }
             Hop lastHop = request.getHop(currentHopNumber);
@@ -318,16 +313,22 @@ public class TransportGraphExploreAction extends HandledTransportAction<GraphExp
             // Execute the search
             SearchSourceBuilder source = new SearchSourceBuilder().query(rootBool).aggregation(sampleAgg).size(0);
             if (request.timeout() != null) {
-                source.timeout(TimeValue.timeValueMillis(timeRemainingMillis()));
+                // Actual resolution of timer is granularity of the interval
+                // configured globally for updating estimated time.
+                long timeRemainingMillis = startTime + request.timeout().millis() - threadPool.relativeTimeInMillis();
+                if (timeRemainingMillis <= 0) {
+                    listener.onResponse(buildResponse(true));
+                    return;
+                }
+
+                source.timeout(TimeValue.timeValueMillis(timeRemainingMillis));
             }
             searchRequest.source(source);
 
-            // System.out.println(source);
             logger.trace("executing expansion graph search request");
             client.search(searchRequest, new ActionListener.Delegating<>(listener) {
                 @Override
                 public void onResponse(SearchResponse searchResponse) {
-                    // System.out.println(searchResponse);
                     addShardFailures(searchResponse.getShardFailures());
 
                     ArrayList<Connection> newConnections = new ArrayList<Connection>();
@@ -676,7 +677,6 @@ public class TransportGraphExploreAction extends HandledTransportAction<GraphExp
                     source.timeout(request.timeout());
                 }
                 searchRequest.source(source);
-                // System.out.println(source);
                 logger.trace("executing initial graph search request");
                 client.search(searchRequest, new ActionListener.Delegating<>(listener) {
                     @Override
@@ -774,16 +774,6 @@ public class TransportGraphExploreAction extends HandledTransportAction<GraphExp
             }
         }
 
-        boolean hasTimedOut() {
-            return request.timeout() != null && (timeRemainingMillis() <= 0);
-        }
-
-        long timeRemainingMillis() {
-            // Actual resolution of timer is granularity of the interval
-            // configured globally for updating estimated time.
-            return (startTime + request.timeout().millis()) - threadPool.relativeTimeInMillis();
-        }
-
         void addShardFailures(ShardOperationFailedException[] failures) {
             if (CollectionUtils.isEmpty(failures) == false) {
                 ShardOperationFailedException[] duplicates = new ShardOperationFailedException[shardFailures.length + failures.length];
@@ -793,9 +783,9 @@ public class TransportGraphExploreAction extends HandledTransportAction<GraphExp
             }
         }
 
-        protected GraphExploreResponse buildResponse() {
+        protected GraphExploreResponse buildResponse(boolean timedOut) {
             long took = threadPool.relativeTimeInMillis() - startTime;
-            return new GraphExploreResponse(took, timedOut.get(), shardFailures, vertices, connections, request.returnDetailedInfo());
+            return new GraphExploreResponse(took, timedOut, shardFailures, vertices, connections, request.returnDetailedInfo());
         }
 
     }