diff --git a/core/src/main/scala/org/apache/spark/deploy/SparkSubmit.scala b/core/src/main/scala/org/apache/spark/deploy/SparkSubmit.scala
index 4baf032f0e9c6..a46af26feb061 100644
--- a/core/src/main/scala/org/apache/spark/deploy/SparkSubmit.scala
+++ b/core/src/main/scala/org/apache/spark/deploy/SparkSubmit.scala
@@ -430,18 +430,15 @@ private[spark] class SparkSubmit extends Logging {
         // Usage: PythonAppRunner <main python file> <extra python files> [app arguments]
         args.mainClass = "org.apache.spark.deploy.PythonRunner"
         args.childArgs = ArrayBuffer(localPrimaryResource, localPyFiles) ++ args.childArgs
-        if (clusterManager != YARN) {
-          // The YARN backend distributes the primary file differently, so don't merge it.
-          args.files = mergeFileLists(args.files, args.primaryResource)
-        }
       }
       if (clusterManager != YARN) {
         // The YARN backend handles python files differently, so don't merge the lists.
         args.files = mergeFileLists(args.files, args.pyFiles)
       }
-      if (localPyFiles != null) {
-        sparkConf.set("spark.submit.pyFiles", localPyFiles)
-      }
+    }
+
+    if (localPyFiles != null) {
+      sparkConf.set("spark.submit.pyFiles", localPyFiles)
     }
 
     // In YARN mode for an R app, add the SparkR package archive and the R package
diff --git a/core/src/main/scala/org/apache/spark/deploy/SparkSubmitArguments.scala b/core/src/main/scala/org/apache/spark/deploy/SparkSubmitArguments.scala
index fed4e0a5069c3..fb232101114b9 100644
--- a/core/src/main/scala/org/apache/spark/deploy/SparkSubmitArguments.scala
+++ b/core/src/main/scala/org/apache/spark/deploy/SparkSubmitArguments.scala
@@ -182,6 +182,7 @@ private[deploy] class SparkSubmitArguments(args: Seq[String], env: Map[String, S
     name = Option(name).orElse(sparkProperties.get("spark.app.name")).orNull
     jars = Option(jars).orElse(sparkProperties.get("spark.jars")).orNull
     files = Option(files).orElse(sparkProperties.get("spark.files")).orNull
+    pyFiles = Option(pyFiles).orElse(sparkProperties.get("spark.submit.pyFiles")).orNull
     ivyRepoPath = sparkProperties.get("spark.jars.ivy").orNull
     ivySettingsPath = sparkProperties.get("spark.jars.ivySettings")
     packages = Option(packages).orElse(sparkProperties.get("spark.jars.packages")).orNull
@@ -280,9 +281,6 @@ private[deploy] class SparkSubmitArguments(args: Seq[String], env: Map[String, S
       numExecutors != null && Try(numExecutors.toInt).getOrElse(-1) <= 0) {
       error("Number of executors must be a positive number")
     }
-    if (pyFiles != null && !isPython) {
-      error("--py-files given but primary resource is not a Python script")
-    }
 
     if (master.startsWith("yarn")) {
       val hasHadoopEnv = env.contains("HADOOP_CONF_DIR") || env.contains("YARN_CONF_DIR")
diff --git a/core/src/test/scala/org/apache/spark/deploy/SparkSubmitSuite.scala b/core/src/test/scala/org/apache/spark/deploy/SparkSubmitSuite.scala
index 43286953e4383..545c8d0423dc3 100644
--- a/core/src/test/scala/org/apache/spark/deploy/SparkSubmitSuite.scala
+++ b/core/src/test/scala/org/apache/spark/deploy/SparkSubmitSuite.scala
@@ -771,9 +771,13 @@ class SparkSubmitSuite
       PythonRunner.formatPaths(Utils.resolveURIs(pyFiles)).mkString(","))
 
     // Test remote python files
+    val hadoopConf = new Configuration()
+    updateConfWithFakeS3Fs(hadoopConf)
     val f4 = File.createTempFile("test-submit-remote-python-files", "", tmpDir)
+    val pyFile1 = File.createTempFile("file1", ".py", tmpDir)
+    val pyFile2 = File.createTempFile("file2", ".py", tmpDir)
     val writer4 = new PrintWriter(f4)
-    val remotePyFiles = "hdfs:///tmp/file1.py,hdfs:///tmp/file2.py"
+    val remotePyFiles = s"s3a://${pyFile1.getAbsolutePath},s3a://${pyFile2.getAbsolutePath}"
     writer4.println("spark.submit.pyFiles " + remotePyFiles)
     writer4.close()
     val clArgs4 = Seq(
@@ -783,7 +787,7 @@ class SparkSubmitSuite
       "hdfs:///tmp/mister.py"
     )
     val appArgs4 = new SparkSubmitArguments(clArgs4)
-    val (_, _, conf4, _) = submit.prepareSubmitEnvironment(appArgs4)
+    val (_, _, conf4, _) = submit.prepareSubmitEnvironment(appArgs4, conf = Some(hadoopConf))
     // Should not format python path for yarn cluster mode
     conf4.get("spark.submit.pyFiles") should be(Utils.resolveURIs(remotePyFiles))
   }
@@ -1093,6 +1097,44 @@ class SparkSubmitSuite
     assert(exception.getMessage() === "hello")
   }
 
+  test("support --py-files/spark.submit.pyFiles in non pyspark application") {
+    val hadoopConf = new Configuration()
+    updateConfWithFakeS3Fs(hadoopConf)
+
+    val tmpDir = Utils.createTempDir()
+    val pyFile = File.createTempFile("tmpPy", ".egg", tmpDir)
+
+    val args = Seq(
+      "--class", UserClasspathFirstTest.getClass.getName.stripPrefix("$"),
+      "--name", "testApp",
+      "--master", "yarn",
+      "--deploy-mode", "client",
+      "--py-files", s"s3a://${pyFile.getAbsolutePath}",
+      "spark-internal"
+    )
+
+    val appArgs = new SparkSubmitArguments(args)
+    val (_, _, conf, _) = submit.prepareSubmitEnvironment(appArgs, conf = Some(hadoopConf))
+
+    conf.get(PY_FILES.key) should be (s"s3a://${pyFile.getAbsolutePath}")
+    conf.get("spark.submit.pyFiles") should (startWith("/"))
+
+    // Verify "spark.submit.pyFiles"
+    val args1 = Seq(
+      "--class", UserClasspathFirstTest.getClass.getName.stripPrefix("$"),
+      "--name", "testApp",
+      "--master", "yarn",
+      "--deploy-mode", "client",
+      "--conf", s"spark.submit.pyFiles=s3a://${pyFile.getAbsolutePath}",
+      "spark-internal"
+    )
+
+    val appArgs1 = new SparkSubmitArguments(args1)
+    val (_, _, conf1, _) = submit.prepareSubmitEnvironment(appArgs1, conf = Some(hadoopConf))
+
+    conf1.get(PY_FILES.key) should be (s"s3a://${pyFile.getAbsolutePath}")
+    conf1.get("spark.submit.pyFiles") should (startWith("/"))
+  }
 }
 
 object SparkSubmitSuite extends SparkFunSuite with TimeLimits {