diff --git a/pinot-core/src/main/java/org/apache/pinot/core/plan/GlobalPlanImplV0.java b/pinot-core/src/main/java/org/apache/pinot/core/plan/GlobalPlanImplV0.java
index d0f06c18f915..832b9beede0a 100644
--- a/pinot-core/src/main/java/org/apache/pinot/core/plan/GlobalPlanImplV0.java
+++ b/pinot-core/src/main/java/org/apache/pinot/core/plan/GlobalPlanImplV0.java
@@ -18,6 +18,7 @@
  */
 package org.apache.pinot.core.plan;
 
+import java.util.concurrent.TimeoutException;
 import org.apache.pinot.common.utils.DataTable;
 import org.apache.pinot.core.operator.InstanceResponseOperator;
 import org.apache.pinot.core.operator.blocks.InstanceResponseBlock;
@@ -45,11 +46,15 @@ public PlanNode getPlanNode() {
   }
 
   @Override
-  public DataTable execute() {
+  public DataTable execute()
+      throws TimeoutException {
     long startTime = System.currentTimeMillis();
     InstanceResponseOperator instanceResponseOperator = _instanceResponsePlanNode.run();
     long endTime1 = System.currentTimeMillis();
     LOGGER.debug("InstanceResponsePlanNode.run() took: {}ms", endTime1 - startTime);
+    if (endTime1 > _instanceResponsePlanNode._queryContext.getEndTimeMs()) {
+      throw new TimeoutException("Query timed out while generating physical execution plan");
+    }
     InstanceResponseBlock instanceResponseBlock = instanceResponseOperator.nextBlock();
     long endTime2 = System.currentTimeMillis();
     LOGGER.debug("InstanceResponseOperator.nextBlock() took: {}ms", endTime2 - endTime1);
diff --git a/pinot-core/src/main/java/org/apache/pinot/core/plan/Plan.java b/pinot-core/src/main/java/org/apache/pinot/core/plan/Plan.java
index 6ea877064d14..00ffe0674ee0 100644
--- a/pinot-core/src/main/java/org/apache/pinot/core/plan/Plan.java
+++ b/pinot-core/src/main/java/org/apache/pinot/core/plan/Plan.java
@@ -18,6 +18,7 @@
  */
 package org.apache.pinot.core.plan;
 
+import java.util.concurrent.TimeoutException;
 import org.apache.pinot.common.utils.DataTable;
 import org.apache.pinot.spi.annotations.InterfaceAudience;
 
@@ -32,5 +33,6 @@ public interface Plan {
   PlanNode getPlanNode();
 
   /** Execute the query plan and get the instance response. */
-  DataTable execute();
+  DataTable execute()
+      throws TimeoutException;
 }
diff --git a/pinot-core/src/test/java/org/apache/pinot/queries/BaseQueriesTest.java b/pinot-core/src/test/java/org/apache/pinot/queries/BaseQueriesTest.java
index 2ce3d903d703..e73069eb69e9 100644
--- a/pinot-core/src/test/java/org/apache/pinot/queries/BaseQueriesTest.java
+++ b/pinot-core/src/test/java/org/apache/pinot/queries/BaseQueriesTest.java
@@ -24,6 +24,7 @@
 import java.util.Map;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
+import java.util.concurrent.TimeoutException;
 import javax.annotation.Nullable;
 import org.apache.pinot.common.request.BrokerRequest;
 import org.apache.pinot.common.request.PinotQuery;
@@ -196,8 +197,13 @@ private BrokerResponseNative getBrokerResponse(PinotQuery pinotQuery, PlanMaker
     // Server side
     serverQueryContext.setEndTimeMs(System.currentTimeMillis() + Server.DEFAULT_QUERY_EXECUTOR_TIMEOUT_MS);
     Plan plan = planMaker.makeInstancePlan(getIndexSegments(), serverQueryContext, EXECUTOR_SERVICE, null);
-    DataTable instanceResponse =
-        queryContext.isExplain() ? ServerQueryExecutorV1Impl.processExplainPlanQueries(plan) : plan.execute();
+    DataTable instanceResponse;
+    try {
+      instanceResponse =
+          queryContext.isExplain() ? ServerQueryExecutorV1Impl.processExplainPlanQueries(plan) : plan.execute();
+    } catch (TimeoutException e) {
+      throw new RuntimeException(e);
+    }
 
     // Broker side
     // Use 2 Threads for 2 data-tables
@@ -264,10 +270,20 @@ private BrokerResponseNative getBrokerResponseDistinctInstances(PinotQuery pinot
     Plan plan1 = planMaker.makeInstancePlan(instances.get(0), serverQueryContext, EXECUTOR_SERVICE, null);
     Plan plan2 = planMaker.makeInstancePlan(instances.get(1), serverQueryContext, EXECUTOR_SERVICE, null);
 
-    DataTable instanceResponse1 =
-        queryContext.isExplain() ? ServerQueryExecutorV1Impl.processExplainPlanQueries(plan1) : plan1.execute();
-    DataTable instanceResponse2 =
-        queryContext.isExplain() ? ServerQueryExecutorV1Impl.processExplainPlanQueries(plan2) : plan2.execute();
+    DataTable instanceResponse1;
+    try {
+      instanceResponse1 =
+          queryContext.isExplain() ? ServerQueryExecutorV1Impl.processExplainPlanQueries(plan1) : plan1.execute();
+    } catch (TimeoutException e) {
+      throw new RuntimeException(e);
+    }
+    DataTable instanceResponse2;
+    try {
+      instanceResponse2 =
+          queryContext.isExplain() ? ServerQueryExecutorV1Impl.processExplainPlanQueries(plan2) : plan2.execute();
+    } catch (TimeoutException e) {
+      throw new RuntimeException(e);
+    }
 
     // Broker side
     // Use 2 Threads for 2 data-tables