diff --git a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/js/ir/KotlinJsIrLink.kt b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/js/ir/KotlinJsIrLink.kt
index b099c23263f..f539bfe5b91 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/js/ir/KotlinJsIrLink.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/js/ir/KotlinJsIrLink.kt
@@ -282,6 +282,23 @@ internal class CacheBuilder(
         if (file in visitedFiles) return
         val compilerArgs = compilerArgsFactory()
         kotlinOptions.copyFreeCompilerArgsToArgs(compilerArgs)
+        var prevIndex: Int? = null
+        compilerArgs.freeArgs = compilerArgs.freeArgs
+            .filterIndexed { index, arg ->
+                !listOf("-source-map-base-dirs", "-source-map-prefix").any {
+                    if (prevIndex != null) {
+                        prevIndex = null
+                        return@any true
+                    }
+                    if (arg.startsWith(it)) {
+                        prevIndex = index
+                        return@any true
+                    }
+
+                    false
+                }
+            }
+
         compilerArgs.freeArgs = compilerArgs.freeArgs
             .filterNot { arg ->
                 IGNORED_ARGS.any {