diff --git a/idea/src/META-INF/plugin.xml b/idea/src/META-INF/plugin.xml
index 357797340a6..f9579e44fd5 100644
--- a/idea/src/META-INF/plugin.xml
+++ b/idea/src/META-INF/plugin.xml
@@ -2056,6 +2056,8 @@
 
     <deadCode implementation="org.jetbrains.kotlin.idea.inspections.KotlinJUnitStaticEntryPoint"/>
 
+    <externalSystemTaskNotificationListener implementation="org.jetbrains.kotlin.idea.configuration.KotlinExternalSystemSyncListener"/>
+
     <!--kotlin script specific extensions-->
     <java.shortNamesCache implementation="org.jetbrains.kotlin.idea.core.script.dependencies.JavaClassesInScriptDependenciesShortNameCache"/>
     <indexedRootsProvider implementation="org.jetbrains.kotlin.idea.core.script.dependencies.KotlinScriptDependenciesIndexableSetContributor"/>
diff --git a/idea/src/org/jetbrains/kotlin/idea/configuration/KotlinExternalSystemSyncListener.kt b/idea/src/org/jetbrains/kotlin/idea/configuration/KotlinExternalSystemSyncListener.kt
new file mode 100644
index 00000000000..3de77cf68db
--- /dev/null
+++ b/idea/src/org/jetbrains/kotlin/idea/configuration/KotlinExternalSystemSyncListener.kt
@@ -0,0 +1,40 @@
+/*
+ * Copyright 2010-2017 JetBrains s.r.o.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.jetbrains.kotlin.idea.configuration
+
+import com.intellij.openapi.externalSystem.model.task.ExternalSystemTaskId
+import com.intellij.openapi.externalSystem.model.task.ExternalSystemTaskNotificationListenerAdapter
+import com.intellij.openapi.externalSystem.model.task.ExternalSystemTaskType
+import org.jetbrains.kotlin.idea.configuration.ui.KotlinConfigurationCheckerComponent
+
+class KotlinExternalSystemSyncListener : ExternalSystemTaskNotificationListenerAdapter() {
+    override fun onStart(id: ExternalSystemTaskId) {
+        if (id.type == ExternalSystemTaskType.RESOLVE_PROJECT) {
+            id.findProject()?.let { project ->
+                KotlinConfigurationCheckerComponent.getInstance(project).syncStarted()
+            }
+        }
+    }
+
+    override fun onEnd(id: ExternalSystemTaskId) {
+        if (id.type == ExternalSystemTaskType.RESOLVE_PROJECT) {
+            id.findProject()?.let { project ->
+                KotlinConfigurationCheckerComponent.getInstance(project).syncDone()
+            }
+        }
+    }
+}
diff --git a/idea/src/org/jetbrains/kotlin/idea/configuration/KotlinSetupEnvironmentNotificationProvider.kt b/idea/src/org/jetbrains/kotlin/idea/configuration/KotlinSetupEnvironmentNotificationProvider.kt
index 743c4dc12c1..bb8e2fe0354 100644
--- a/idea/src/org/jetbrains/kotlin/idea/configuration/KotlinSetupEnvironmentNotificationProvider.kt
+++ b/idea/src/org/jetbrains/kotlin/idea/configuration/KotlinSetupEnvironmentNotificationProvider.kt
@@ -39,6 +39,7 @@ import com.intellij.ui.EditorNotificationPanel
 import com.intellij.ui.EditorNotifications
 import org.jetbrains.kotlin.idea.KotlinFileType
 import org.jetbrains.kotlin.idea.KotlinLanguage
+import org.jetbrains.kotlin.idea.configuration.ui.KotlinConfigurationCheckerComponent
 import org.jetbrains.kotlin.idea.util.application.runWriteAction
 import org.jetbrains.kotlin.idea.versions.UnsupportedAbiVersionNotificationPanelProvider
 import org.jetbrains.kotlin.idea.versions.createComponentActionLabel
@@ -77,7 +78,8 @@ class KotlinSetupEnvironmentNotificationProvider(
             return createSetupSdkPanel(myProject, psiFile)
         }
 
-        if (!hasAnyKotlinRuntimeInScope(module) &&
+        if (!KotlinConfigurationCheckerComponent.getInstance(module.project).isSyncing &&
+            !hasAnyKotlinRuntimeInScope(module) &&
             UnsupportedAbiVersionNotificationPanelProvider.collectBadRoots(module).isEmpty()) {
             return createKotlinNotConfiguredPanel(module)
         }
diff --git a/idea/src/org/jetbrains/kotlin/idea/configuration/ui/KotlinConfigurationCheckerComponent.kt b/idea/src/org/jetbrains/kotlin/idea/configuration/ui/KotlinConfigurationCheckerComponent.kt
index 189537a30a9..28557f6973d 100644
--- a/idea/src/org/jetbrains/kotlin/idea/configuration/ui/KotlinConfigurationCheckerComponent.kt
+++ b/idea/src/org/jetbrains/kotlin/idea/configuration/ui/KotlinConfigurationCheckerComponent.kt
@@ -24,9 +24,10 @@ import com.intellij.openapi.project.Project
 import com.intellij.openapi.startup.StartupManager
 import org.jetbrains.kotlin.idea.configuration.*
 import org.jetbrains.kotlin.idea.versions.*
-import org.jetbrains.kotlin.idea.versions.VersionedLibrary
+import java.util.concurrent.atomic.AtomicInteger
 
 class KotlinConfigurationCheckerComponent protected constructor(project: Project) : AbstractProjectComponent(project) {
+    private var syncCount = AtomicInteger()
 
     init {
         NotificationsConfiguration.getNotificationsConfiguration().register(CONFIGURE_NOTIFICATION_GROUP_ID, NotificationDisplayType.STICKY_BALLOON, true)
@@ -41,13 +42,35 @@ class KotlinConfigurationCheckerComponent protected constructor(project: Project
                 if (!libraries.isEmpty()) {
                     notifyOutdatedKotlinRuntime(myProject, libraries)
                 }
-                showConfigureKotlinNotificationIfNeeded(myProject,
-                                                        collectModulesWithOutdatedRuntime(libraries))
+                if (syncCount.get() == 0) {
+                    showConfigureKotlinNotificationIfNeeded(myProject,
+                                                            collectModulesWithOutdatedRuntime(libraries))
+                }
+            }
+        }
+    }
+
+    val isSyncing: Boolean get() = syncCount.get() > 0
+
+    fun syncStarted() {
+        syncCount.incrementAndGet()
+    }
+
+    fun syncDone() {
+        if (syncCount.decrementAndGet() == 0) {
+            DumbService.getInstance(myProject).smartInvokeLater {
+                if (!isSyncing) {
+                    showConfigureKotlinNotificationIfNeeded(myProject,
+                                                            collectModulesWithOutdatedRuntime(findOutdatedKotlinLibraries(myProject)))
+                }
             }
         }
     }
 
     companion object {
         val CONFIGURE_NOTIFICATION_GROUP_ID = "Configure Kotlin in Project"
+
+        fun getInstance(project: Project): KotlinConfigurationCheckerComponent
+                = project.getComponent(KotlinConfigurationCheckerComponent::class.java)
     }
 }