diff --git a/sql/core/src/main/scala/org/apache/spark/sql/execution/streaming/CheckpointFileManager.scala b/sql/core/src/main/scala/org/apache/spark/sql/execution/streaming/CheckpointFileManager.scala
index b3e4240c315b..285af65f78ca 100644
--- a/sql/core/src/main/scala/org/apache/spark/sql/execution/streaming/CheckpointFileManager.scala
+++ b/sql/core/src/main/scala/org/apache/spark/sql/execution/streaming/CheckpointFileManager.scala
@@ -329,6 +329,8 @@ class FileContextBasedCheckpointFileManager(path: Path, hadoopConf: Configuratio
   override def renameTempFile(srcPath: Path, dstPath: Path, overwriteIfPossible: Boolean): Unit = {
     import Options.Rename._
     fc.rename(srcPath, dstPath, if (overwriteIfPossible) OVERWRITE else NONE)
+    // TODO: this is a workaround of HADOOP-16255 - remove this when HADOOP-16255 is resolved
+    mayRemoveCrcFile(srcPath)
   }
 
 
@@ -345,5 +347,17 @@ class FileContextBasedCheckpointFileManager(path: Path, hadoopConf: Configuratio
     case _: LocalFs | _: RawLocalFs => true // LocalFs = RawLocalFs + ChecksumFs
     case _ => false
   }
+
+  private def mayRemoveCrcFile(path: Path): Unit = {
+    try {
+      val checksumFile = new Path(path.getParent, s".${path.getName}.crc")
+      if (exists(checksumFile)) {
+        // checksum file exists, deleting it
+        delete(checksumFile)
+      }
+    } catch {
+      case NonFatal(_) => // ignore, we are removing crc file as "best-effort"
+    }
+  }
 }
 
diff --git a/sql/core/src/test/scala/org/apache/spark/sql/execution/streaming/CheckpointFileManagerSuite.scala b/sql/core/src/test/scala/org/apache/spark/sql/execution/streaming/CheckpointFileManagerSuite.scala
index fe59cb25d500..ab6fbeda7768 100644
--- a/sql/core/src/test/scala/org/apache/spark/sql/execution/streaming/CheckpointFileManagerSuite.scala
+++ b/sql/core/src/test/scala/org/apache/spark/sql/execution/streaming/CheckpointFileManagerSuite.scala
@@ -78,6 +78,22 @@ abstract class CheckpointFileManagerTests extends SparkFunSuite {
       assert(fm.exists(path))
       fm.createAtomic(path, overwriteIfPossible = true).close()  // should not throw exception
 
+      // crc file should not be leaked when origin file doesn't exist.
+      // The implementation of Hadoop filesystem may filter out checksum file, so
+      // listing files from local filesystem.
+      val fileNames = new File(path.getParent.toString).listFiles().toSeq
+        .filter(p => p.isFile).map(p => p.getName)
+      val crcFiles = fileNames.filter(n => n.startsWith(".") && n.endsWith(".crc"))
+      val originFileNamesForExistingCrcFiles = crcFiles.map { name =>
+        // remove first "." and last ".crc"
+        name.substring(1, name.length - 4)
+      }
+
+      // Check all origin files exist for all crc files.
+      assert(originFileNamesForExistingCrcFiles.toSet.subsetOf(fileNames.toSet),
+        s"Some of origin files for crc files don't exist - crc files: $crcFiles / " +
+          s"expected origin files: $originFileNamesForExistingCrcFiles / actual files: $fileNames")
+
       // Open and delete
       fm.open(path).close()
       fm.delete(path)
diff --git a/sql/core/src/test/scala/org/apache/spark/sql/execution/streaming/HDFSMetadataLogSuite.scala b/sql/core/src/test/scala/org/apache/spark/sql/execution/streaming/HDFSMetadataLogSuite.scala
index 0e36e7f5da12..e832422a93b5 100644
--- a/sql/core/src/test/scala/org/apache/spark/sql/execution/streaming/HDFSMetadataLogSuite.scala
+++ b/sql/core/src/test/scala/org/apache/spark/sql/execution/streaming/HDFSMetadataLogSuite.scala
@@ -26,6 +26,7 @@ import org.scalatest.concurrent.Waiters._
 import org.scalatest.time.SpanSugar._
 
 import org.apache.spark.SparkFunSuite
+import org.apache.spark.sql.internal.SQLConf
 import org.apache.spark.sql.test.SharedSQLContext
 import org.apache.spark.util.UninterruptibleThread
 
@@ -59,6 +60,21 @@ class HDFSMetadataLogSuite extends SparkFunSuite with SharedSQLContext {
   }
 
   test("HDFSMetadataLog: purge") {
+    testPurge()
+  }
+
+  Seq(
+    classOf[FileSystemBasedCheckpointFileManager],
+    classOf[FileContextBasedCheckpointFileManager]
+  ).map(_.getCanonicalName).foreach { cls =>
+    test(s"HDFSMetadataLog: purge - explicit file manager - $cls") {
+      withSQLConf(SQLConf.STREAMING_CHECKPOINT_FILE_MANAGER_CLASS.parent.key -> cls) {
+        testPurge()
+      }
+    }
+  }
+
+  private def testPurge(): Unit = {
     withTempDir { temp =>
       val metadataLog = new HDFSMetadataLog[String](spark, temp.getAbsolutePath)
       assert(metadataLog.add(0, "batch0"))
@@ -75,12 +91,16 @@ class HDFSMetadataLogSuite extends SparkFunSuite with SharedSQLContext {
       assert(metadataLog.get(2).isDefined)
       assert(metadataLog.getLatest().get._1 == 2)
 
-      // There should be exactly one file, called "2", in the metadata directory.
+      // There should be at most two files, called "2", and optionally crc file,
+      // in the metadata directory.
       // This check also tests for regressions of SPARK-17475
-      val allFiles = new File(metadataLog.metadataPath.toString).listFiles()
-        .filter(!_.getName.startsWith(".")).toSeq
-      assert(allFiles.size == 1)
-      assert(allFiles(0).getName() == "2")
+      val allFiles = new File(metadataLog.metadataPath.toString).listFiles().toSeq
+      assert(allFiles.size <= 2)
+      assert(allFiles.exists(_.getName == "2"))
+      if (allFiles.size == 2) {
+        // there's possibly crc file being left as well
+        assert(allFiles.exists(_.getName == ".2.crc"))
+      }
     }
   }