diff --git a/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/config/JvmContentRoots.kt b/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/config/JvmContentRoots.kt
index 4ead353dc32..15d35f26583 100644
--- a/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/config/JvmContentRoots.kt
+++ b/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/config/JvmContentRoots.kt
@@ -26,7 +26,9 @@ interface JvmContentRoot : ContentRoot {
     val file: File
 }
 
-data class JvmClasspathRoot(override val file: File) : JvmContentRoot
+data class JvmClasspathRoot(override val file: File, val isSdkRoot: Boolean) : JvmContentRoot {
+    constructor(file: File) : this(file, false)
+}
 
 data class JavaSourceRoot(override val file: File, val packagePrefix: String?) : JvmContentRoot
 
@@ -41,7 +43,7 @@ fun CompilerConfiguration.addJvmClasspathRoots(files: List<File>) {
 }
 
 fun CompilerConfiguration.addJvmSdkRoots(files: List<File>) {
-    addAll(CLIConfigurationKeys.CONTENT_ROOTS, 0, files.map(::JvmClasspathRoot))
+    addAll(CLIConfigurationKeys.CONTENT_ROOTS, 0, files.map { file -> JvmClasspathRoot(file, true) })
 }
 
 val CompilerConfiguration.jvmClasspathRoots: List<File>
diff --git a/plugins/scripting/scripting-compiler/src/org/jetbrains/kotlin/scripting/compiler/plugin/impl/ScriptJvmCompilerImpls.kt b/plugins/scripting/scripting-compiler/src/org/jetbrains/kotlin/scripting/compiler/plugin/impl/ScriptJvmCompilerImpls.kt
index 9b58d7490c8..3df8268b590 100644
--- a/plugins/scripting/scripting-compiler/src/org/jetbrains/kotlin/scripting/compiler/plugin/impl/ScriptJvmCompilerImpls.kt
+++ b/plugins/scripting/scripting-compiler/src/org/jetbrains/kotlin/scripting/compiler/plugin/impl/ScriptJvmCompilerImpls.kt
@@ -11,6 +11,8 @@ import org.jetbrains.kotlin.cli.common.messages.MessageCollector
 import org.jetbrains.kotlin.cli.jvm.compiler.KotlinCoreEnvironment
 import org.jetbrains.kotlin.cli.jvm.compiler.NoScopeRecordCliBindingTrace
 import org.jetbrains.kotlin.cli.jvm.compiler.TopDownAnalyzerFacadeForJVM
+import org.jetbrains.kotlin.cli.jvm.config.JvmClasspathRoot
+import org.jetbrains.kotlin.cli.jvm.config.JvmContentRoot
 import org.jetbrains.kotlin.cli.jvm.config.jvmClasspathRoots
 import org.jetbrains.kotlin.codegen.ClassBuilderFactories
 import org.jetbrains.kotlin.codegen.KotlinCodegenFacade
@@ -126,7 +128,8 @@ private fun compileImpl(
                 // performed with the expected classpath
                 // TODO: make this logic obsolete by injecting classpath earlier in the pipeline
                 val depsFromConfiguration = get(dependencies)?.flatMapTo(HashSet()) { (it as? JvmDependency)?.classpath ?: emptyList() }
-                val depsFromCompiler = context.environment.configuration.jvmClasspathRoots
+                val depsFromCompiler = context.environment.configuration.getList(CLIConfigurationKeys.CONTENT_ROOTS)
+                    .mapNotNull { if (it is JvmClasspathRoot && !it.isSdkRoot) it.file else null }
                 if (!depsFromConfiguration.isNullOrEmpty()) {
                     val missingDeps = depsFromCompiler.filter { !depsFromConfiguration.contains(it) }
                     if (missingDeps.isNotEmpty()) {