diff --git a/jps/jps-plugin/jps-tests/test/org/jetbrains/kotlin/jps/build/KotlinJpsBuildTest.kt b/jps/jps-plugin/jps-tests/test/org/jetbrains/kotlin/jps/build/KotlinJpsBuildTest.kt
index f6d3c0a0c09..62fb117a963 100644
--- a/jps/jps-plugin/jps-tests/test/org/jetbrains/kotlin/jps/build/KotlinJpsBuildTest.kt
+++ b/jps/jps-plugin/jps-tests/test/org/jetbrains/kotlin/jps/build/KotlinJpsBuildTest.kt
@@ -946,6 +946,12 @@ open class KotlinJpsBuildTest : KotlinJpsBuildTestBase() {
         checkWhen(emptyArray(), null, packageClasses("kotlinProject", "src/test1.kt", "Test1Kt"))
     }
 
+    @WorkingDir("KotlinProjectWithSingleKotlinFileAsSourceRoot")
+    fun testBuildProjectWithSingleKotlinFileAsSource() {
+        initProject(JVM_MOCK_RUNTIME)
+        buildAllModules().assertSuccessful()
+    }
+
     fun testBuildAfterGdwBuild() {
         initProject(JVM_FULL_RUNTIME)
         findModule("module2").let {
diff --git a/jps/jps-plugin/src/org/jetbrains/kotlin/jps/targets/KotlinJvmModuleBuildTarget.kt b/jps/jps-plugin/src/org/jetbrains/kotlin/jps/targets/KotlinJvmModuleBuildTarget.kt
index 138bd3a9fbb..ef251088979 100644
--- a/jps/jps-plugin/src/org/jetbrains/kotlin/jps/targets/KotlinJvmModuleBuildTarget.kt
+++ b/jps/jps-plugin/src/org/jetbrains/kotlin/jps/targets/KotlinJvmModuleBuildTarget.kt
@@ -202,7 +202,7 @@ class KotlinJvmModuleBuildTarget(kotlinContext: KotlinCompileContext, jpsModuleB
                 kotlinModuleId.name,
                 outputDir.absolutePath,
                 preprocessSources(allFiles),
-                target.findSourceRoots(dirtyFilesHolder.context),
+                target.findJavaSourceRoots(dirtyFilesHolder.context),
                 target.findClassPathRoots(),
                 preprocessSources(commonSourceFiles),
                 target.findModularJdkRoot(),
@@ -327,13 +327,14 @@ class KotlinJvmModuleBuildTarget(kotlinContext: KotlinCompileContext, jpsModuleB
         return File(url.substringAfter(URLUtil.JRT_PROTOCOL + URLUtil.SCHEME_SEPARATOR).substringBeforeLast(URLUtil.JAR_SEPARATOR))
     }
 
-    private fun findSourceRoots(context: CompileContext): List<JvmSourceRoot> {
+    private fun findJavaSourceRoots(context: CompileContext): List<JvmSourceRoot> {
         val roots = context.projectDescriptor.buildRootIndex.getTargetRoots(jpsModuleBuildTarget, context)
         val result = mutableListOf<JvmSourceRoot>()
         for (root in roots) {
             val file = root.rootFile
+            val filePath = file.toPath()
             val prefix = root.packagePrefix
-            if (Files.exists(file.toPath())) {
+            if (Files.exists(filePath) && (Files.isDirectory(filePath) || file.extension == "java")) {
                 result.add(JvmSourceRoot(file, prefix.ifEmpty { null }))
             }
         }
diff --git a/jps/jps-plugin/testData/general/KotlinProjectWithSingleKotlinFileAsSourceRoot/kotlinProject.iml b/jps/jps-plugin/testData/general/KotlinProjectWithSingleKotlinFileAsSourceRoot/kotlinProject.iml
new file mode 100644
index 00000000000..28b61f9b5d3
--- /dev/null
+++ b/jps/jps-plugin/testData/general/KotlinProjectWithSingleKotlinFileAsSourceRoot/kotlinProject.iml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="JAVA_MODULE" version="4">
+  <component name="NewModuleRootManager" inherit-compiler-output="true">
+    <exclude-output />
+    <content url="file://$MODULE_DIR$/src/test1.kt">
+      <sourceFolder url="file://$MODULE_DIR$/src/test1.kt" isTestSource="false" />
+    </content>
+    <orderEntry type="jdk" jdkName="IDEA_JDK" jdkType="JavaSDK" />
+    <orderEntry type="sourceFolder" forTests="false" />
+    <orderEntry type="module" module-name="kotlinProject" />
+  </component>
+</module>
diff --git a/jps/jps-plugin/testData/general/KotlinProjectWithSingleKotlinFileAsSourceRoot/kotlinProject.ipr b/jps/jps-plugin/testData/general/KotlinProjectWithSingleKotlinFileAsSourceRoot/kotlinProject.ipr
new file mode 100644
index 00000000000..e02c0c30a2f
--- /dev/null
+++ b/jps/jps-plugin/testData/general/KotlinProjectWithSingleKotlinFileAsSourceRoot/kotlinProject.ipr
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="CompilerConfiguration">
+    <option name="DEFAULT_COMPILER" value="Javac" />
+  </component>
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/kotlinProject.iml" filepath="$PROJECT_DIR$/kotlinProject.iml" />
+    </modules>
+  </component>
+  <component name="ProjectRootManager" version="2" languageLevel="JDK_1_8" assert-keyword="true" jdk-15="true" project-jdk-name="IDEA_JDK" project-jdk-type="JavaSDK">
+    <output url="file://$PROJECT_DIR$/out" />
+  </component>
+</project>
\ No newline at end of file
diff --git a/jps/jps-plugin/testData/general/KotlinProjectWithSingleKotlinFileAsSourceRoot/src/test1.kt b/jps/jps-plugin/testData/general/KotlinProjectWithSingleKotlinFileAsSourceRoot/src/test1.kt
new file mode 100644
index 00000000000..a2c4e958bb5
--- /dev/null
+++ b/jps/jps-plugin/testData/general/KotlinProjectWithSingleKotlinFileAsSourceRoot/src/test1.kt
@@ -0,0 +1,3 @@
+fun foo() {
+
+}
\ No newline at end of file