diff --git a/sql/catalyst/src/main/scala/org/apache/spark/sql/catalyst/plans/logical/basicLogicalOperators.scala b/sql/catalyst/src/main/scala/org/apache/spark/sql/catalyst/plans/logical/basicLogicalOperators.scala
index b4c6e19d0bc39..677bdf2733612 100644
--- a/sql/catalyst/src/main/scala/org/apache/spark/sql/catalyst/plans/logical/basicLogicalOperators.scala
+++ b/sql/catalyst/src/main/scala/org/apache/spark/sql/catalyst/plans/logical/basicLogicalOperators.scala
@@ -1369,7 +1369,8 @@ case class SubqueryAlias(
 
   override def metadataOutput: Seq[Attribute] = {
     val qualifierList = identifier.qualifier :+ alias
-    child.metadataOutput.map(_.withQualifier(qualifierList))
+    val nonHiddenMetadataOutput = child.metadataOutput.filter(!_.supportsQualifiedStar)
+    nonHiddenMetadataOutput.map(_.withQualifier(qualifierList))
   }
 
   override def maxRows: Option[Long] = child.maxRows
diff --git a/sql/core/src/test/scala/org/apache/spark/sql/DataFrameJoinSuite.scala b/sql/core/src/test/scala/org/apache/spark/sql/DataFrameJoinSuite.scala
index 5286a70674e78..de900fffb34a3 100644
--- a/sql/core/src/test/scala/org/apache/spark/sql/DataFrameJoinSuite.scala
+++ b/sql/core/src/test/scala/org/apache/spark/sql/DataFrameJoinSuite.scala
@@ -554,4 +554,26 @@ class DataFrameJoinSuite extends QueryTest
       )
     }
   }
+
+  test("SPARK-39376: Hide duplicated columns in star expansion of subquery alias from USING JOIN") {
+    val joinDf = testData2.as("testData2").join(
+      testData3.as("testData3"), usingColumns = Seq("a"), joinType = "fullouter")
+    val equivalentQueries = Seq(
+      joinDf.select($"*"),
+      joinDf.as("r").select($"*"),
+      joinDf.as("r").select($"r.*")
+    )
+    equivalentQueries.foreach { query =>
+      checkAnswer(query,
+        Seq(
+          Row(1, 1, null),
+          Row(1, 2, null),
+          Row(2, 1, 2),
+          Row(2, 2, 2),
+          Row(3, 1, null),
+          Row(3, 2, null)
+        )
+      )
+    }
+  }
 }