diff --git a/java/flight/flight-sql-jdbc-core/src/main/java/org/apache/arrow/driver/jdbc/utils/FlightEndpointDataQueue.java b/java/flight/flight-sql-jdbc-core/src/main/java/org/apache/arrow/driver/jdbc/utils/FlightEndpointDataQueue.java
index 71cafd2ec3075..1198d89c40aef 100644
--- a/java/flight/flight-sql-jdbc-core/src/main/java/org/apache/arrow/driver/jdbc/utils/FlightEndpointDataQueue.java
+++ b/java/flight/flight-sql-jdbc-core/src/main/java/org/apache/arrow/driver/jdbc/utils/FlightEndpointDataQueue.java
@@ -104,9 +104,8 @@ private CloseableEndpointStreamPair next(final EndpointStreamSupplier endpointSt
       futures.remove(future);
       try {
         final CloseableEndpointStreamPair endpoint = future.get();
-        // Get the next FlightStream with content.
-        // The stream is non-empty.
-        if (endpoint.getStream().getRoot().getRowCount() > 0) {
+        // Get the next FlightStream that has a root with content.
+        if (endpoint != null) {
           return endpoint;
         }
       } catch (final ExecutionException | InterruptedException | CancellationException e) {
@@ -178,8 +177,12 @@ public synchronized void enqueue(final CloseableEndpointStreamPair endpointReque
     endpointsToClose.add(endpointRequest);
     futures.add(completionService.submit(() -> {
       // `FlightStream#next` will block until new data can be read or stream is over.
-      endpointRequest.getStream().next();
-      return endpointRequest;
+      while (endpointRequest.getStream().next()) {
+        if (endpointRequest.getStream().getRoot().getRowCount() > 0) {
+          return endpointRequest;
+        }
+      }
+      return null;
     }));
   }
 
diff --git a/java/flight/flight-sql-jdbc-core/src/test/java/org/apache/arrow/driver/jdbc/ResultSetTest.java b/java/flight/flight-sql-jdbc-core/src/test/java/org/apache/arrow/driver/jdbc/ResultSetTest.java
index e2ac100b8dc36..5b9e269fb3cc8 100644
--- a/java/flight/flight-sql-jdbc-core/src/test/java/org/apache/arrow/driver/jdbc/ResultSetTest.java
+++ b/java/flight/flight-sql-jdbc-core/src/test/java/org/apache/arrow/driver/jdbc/ResultSetTest.java
@@ -455,4 +455,17 @@ allocator, forGrpcInsecure("localhost", 0), rootProducer)
       }
     }
   }
+
+  @Test
+  public void testShouldRunSelectQueryWithEmptyVectorsEmbedded() throws Exception {
+    try (Statement statement = connection.createStatement();
+         ResultSet resultSet = statement.executeQuery(
+             CoreMockedSqlProducers.LEGACY_REGULAR_WITH_EMPTY_SQL_CMD)) {
+      long rowCount = 0;
+      while (resultSet.next()) {
+        ++rowCount;
+      }
+      assertEquals(2, rowCount);
+    }
+  }
 }
diff --git a/java/flight/flight-sql-jdbc-core/src/test/java/org/apache/arrow/driver/jdbc/utils/CoreMockedSqlProducers.java b/java/flight/flight-sql-jdbc-core/src/test/java/org/apache/arrow/driver/jdbc/utils/CoreMockedSqlProducers.java
index cf359849a7105..a8e2e7f2e4ce5 100644
--- a/java/flight/flight-sql-jdbc-core/src/test/java/org/apache/arrow/driver/jdbc/utils/CoreMockedSqlProducers.java
+++ b/java/flight/flight-sql-jdbc-core/src/test/java/org/apache/arrow/driver/jdbc/utils/CoreMockedSqlProducers.java
@@ -64,6 +64,7 @@ public final class CoreMockedSqlProducers {
   public static final String LEGACY_REGULAR_SQL_CMD = "SELECT * FROM TEST";
   public static final String LEGACY_METADATA_SQL_CMD = "SELECT * FROM METADATA";
   public static final String LEGACY_CANCELLATION_SQL_CMD = "SELECT * FROM TAKES_FOREVER";
+  public static final String LEGACY_REGULAR_WITH_EMPTY_SQL_CMD = "SELECT * FROM TEST_EMPTIES";
 
   private CoreMockedSqlProducers() {
     // Prevent instantiation.
@@ -80,9 +81,44 @@ public static MockFlightSqlProducer getLegacyProducer() {
     addLegacyRegularSqlCmdSupport(producer);
     addLegacyMetadataSqlCmdSupport(producer);
     addLegacyCancellationSqlCmdSupport(producer);
+    addQueryWithEmbeddedEmptyRoot(producer);
     return producer;
   }
 
+  private static void addQueryWithEmbeddedEmptyRoot(final MockFlightSqlProducer producer) {
+    final Schema querySchema = new Schema(ImmutableList.of(
+        new Field(
+            "ID",
+            new FieldType(true, new ArrowType.Int(64, true),
+                null),
+            null)
+    ));
+
+    final List<Consumer<ServerStreamListener>> resultProducers = new ArrayList<>();
+    Consumer<ServerStreamListener> dataRoot = listener -> {
+      try (final BufferAllocator allocator = new RootAllocator(Long.MAX_VALUE);
+           final VectorSchemaRoot root = VectorSchemaRoot.create(querySchema, allocator)) {
+        root.allocateNew();
+        root.setRowCount(0);
+        listener.start(root);
+        listener.putNext(); // empty root
+        ((BigIntVector) root.getVector("ID")).setSafe(0, 100L);
+        root.setRowCount(1);
+        listener.putNext(); // data root
+        root.clear();
+        root.setRowCount(0);
+        listener.putNext(); // empty root
+        ((BigIntVector) root.getVector("ID")).setSafe(0, 100L);
+        root.setRowCount(1);
+        listener.putNext(); // data root
+      } finally {
+        listener.completed();
+      }
+    };
+    resultProducers.add(dataRoot);
+    producer.addSelectQuery(LEGACY_REGULAR_WITH_EMPTY_SQL_CMD, querySchema, resultProducers);
+  }
+
   private static void addLegacyRegularSqlCmdSupport(final MockFlightSqlProducer producer) {
     final Schema querySchema = new Schema(ImmutableList.of(
         new Field(