diff --git a/hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/CompactSplit.java b/hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/CompactSplit.java
index 441b18b3302f..158b86fd61bc 100644
--- a/hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/CompactSplit.java
+++ b/hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/CompactSplit.java
@@ -24,6 +24,7 @@
 import java.io.IOException;
 import java.io.PrintWriter;
 import java.io.StringWriter;
+import java.util.Collection;
 import java.util.Comparator;
 import java.util.Iterator;
 import java.util.Optional;
@@ -444,14 +445,24 @@ public int getCompactionQueueSize() {
   }
 
   public int getLargeCompactionQueueSize() {
+    removeFilesFromFilesCompacting(longCompactions);
     return longCompactions.getQueue().size();
   }
 
 
   public int getSmallCompactionQueueSize() {
+    removeFilesFromFilesCompacting(shortCompactions);
     return shortCompactions.getQueue().size();
   }
 
+  private void removeFilesFromFilesCompacting(ThreadPoolExecutor compactor) {
+    for (Runnable runnable : compactor.getQueue()) {
+      CompactionRunner runner = (CompactionRunner) runnable;
+      Collection<HStoreFile> files = runner.compaction.getRequest().getFiles();
+      runner.store.removeFromCompactingFiles(files);
+    }
+  }
+
   public int getSplitQueueSize() {
     return splits.getQueue().size();
   }
diff --git a/hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/HStore.java b/hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/HStore.java
index 45b17bb32ad1..648f6fd549e5 100644
--- a/hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/HStore.java
+++ b/hbase-server/src/main/java/org/apache/hadoop/hbase/regionserver/HStore.java
@@ -1953,6 +1953,16 @@ private void addToCompactingFiles(Collection<HStoreFile> filesToAdd) {
     Collections.sort(filesCompacting, storeEngine.getStoreFileManager().getStoreFileComparator());
   }
 
+  /**
+   * remove the files from compacting files. This usually happens when we clear compaction queues.
+   */
+  public void removeFromCompactingFiles(Collection<HStoreFile> filesToRemove) {
+    synchronized (filesCompacting) {
+      filesCompacting.removeAll(filesToRemove);
+      Collections.sort(filesCompacting, storeEngine.getStoreFileManager().getStoreFileComparator());
+    }
+  }
+
   private void removeUnneededFiles() throws IOException {
     if (!conf.getBoolean("hbase.store.delete.expired.storefile", true)) {
       return;