diff --git a/x-pack/plugin/ccr/src/main/java/org/elasticsearch/xpack/ccr/Ccr.java b/x-pack/plugin/ccr/src/main/java/org/elasticsearch/xpack/ccr/Ccr.java
index 13749c2abb6d4..5ca26b5e2d48b 100644
--- a/x-pack/plugin/ccr/src/main/java/org/elasticsearch/xpack/ccr/Ccr.java
+++ b/x-pack/plugin/ccr/src/main/java/org/elasticsearch/xpack/ccr/Ccr.java
@@ -52,6 +52,7 @@
 import org.elasticsearch.xpack.ccr.action.CcrRequests;
 import org.elasticsearch.xpack.ccr.action.ShardChangesAction;
 import org.elasticsearch.xpack.ccr.action.ShardFollowTask;
+import org.elasticsearch.xpack.ccr.action.ShardFollowTaskCleaner;
 import org.elasticsearch.xpack.ccr.action.ShardFollowTasksExecutor;
 import org.elasticsearch.xpack.ccr.action.TransportCcrStatsAction;
 import org.elasticsearch.xpack.ccr.action.TransportDeleteAutoFollowPatternAction;
@@ -182,6 +183,7 @@ public Collection<Object> createComponents(
             ccrLicenseChecker,
             restoreSourceService,
             new CcrRepositoryManager(settings, clusterService, client),
+            new ShardFollowTaskCleaner(clusterService, threadPool, client),
             new AutoFollowCoordinator(
                 settings,
                 client,
diff --git a/x-pack/plugin/ccr/src/main/java/org/elasticsearch/xpack/ccr/action/ShardFollowTaskCleaner.java b/x-pack/plugin/ccr/src/main/java/org/elasticsearch/xpack/ccr/action/ShardFollowTaskCleaner.java
new file mode 100644
index 0000000000000..af704b6741727
--- /dev/null
+++ b/x-pack/plugin/ccr/src/main/java/org/elasticsearch/xpack/ccr/action/ShardFollowTaskCleaner.java
@@ -0,0 +1,85 @@
+/*
+ * Copyright Elasticsearch B.V. and/or licensed to Elasticsearch B.V. under one
+ * or more contributor license agreements. Licensed under the Elastic License;
+ * you may not use this file except in compliance with the Elastic License.
+ */
+
+package org.elasticsearch.xpack.ccr.action;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.elasticsearch.action.ActionListener;
+import org.elasticsearch.client.Client;
+import org.elasticsearch.cluster.ClusterChangedEvent;
+import org.elasticsearch.cluster.ClusterStateListener;
+import org.elasticsearch.cluster.metadata.MetaData;
+import org.elasticsearch.cluster.service.ClusterService;
+import org.elasticsearch.gateway.GatewayService;
+import org.elasticsearch.index.Index;
+import org.elasticsearch.index.IndexNotFoundException;
+import org.elasticsearch.persistent.CompletionPersistentTaskAction;
+import org.elasticsearch.persistent.PersistentTaskResponse;
+import org.elasticsearch.persistent.PersistentTasksCustomMetaData;
+import org.elasticsearch.threadpool.ThreadPool;
+
+/**
+ * A {@link ClusterStateListener} that completes any {@link ShardFollowTask} which concerns a deleted index.
+ */
+public class ShardFollowTaskCleaner implements ClusterStateListener {
+
+    private static final Logger logger = LogManager.getLogger(ShardFollowTaskCleaner.class);
+
+    private final ThreadPool threadPool;
+    private final Client client;
+
+    public ShardFollowTaskCleaner(final ClusterService clusterService, final ThreadPool threadPool, final Client client) {
+        this.threadPool = threadPool;
+        this.client = client;
+        clusterService.addListener(this);
+    }
+
+    @Override
+    public void clusterChanged(final ClusterChangedEvent event) {
+        if (event.state().blocks().hasGlobalBlock(GatewayService.STATE_NOT_RECOVERED_BLOCK)) {
+            return;
+        }
+        if (event.localNodeMaster() == false) {
+            return;
+        }
+
+        MetaData metaData = event.state().metaData();
+        PersistentTasksCustomMetaData persistentTasksMetaData = metaData.custom(PersistentTasksCustomMetaData.TYPE);
+        if (persistentTasksMetaData == null) {
+            return;
+        }
+        for (PersistentTasksCustomMetaData.PersistentTask<?> persistentTask : persistentTasksMetaData.tasks()) {
+            if (ShardFollowTask.NAME.equals(persistentTask.getTaskName()) == false) {
+                // this task is not a shard follow task
+                continue;
+            }
+            ShardFollowTask shardFollowTask = (ShardFollowTask) persistentTask.getParams();
+            Index followerIndex = shardFollowTask.getFollowShardId().getIndex();
+            if (metaData.index(followerIndex) != null) {
+                // the index exists, do not clean this persistent task
+                continue;
+            }
+            IndexNotFoundException e = new IndexNotFoundException(followerIndex);
+            CompletionPersistentTaskAction.Request request =
+                new CompletionPersistentTaskAction.Request(persistentTask.getId(), persistentTask.getAllocationId(), e);
+            threadPool.generic().submit(() -> {
+                client.execute(CompletionPersistentTaskAction.INSTANCE, request, new ActionListener<>() {
+
+                    @Override
+                    public void onResponse(PersistentTaskResponse persistentTaskResponse) {
+                        logger.debug("task [{}] cleaned up", persistentTask.getId());
+                    }
+
+                    @Override
+                    public void onFailure(Exception e) {
+                        logger.warn("failed to clean up task [{}]", persistentTask.getId());
+                    }
+                });
+            });
+        }
+    }
+}
diff --git a/x-pack/plugin/ccr/src/test/java/org/elasticsearch/xpack/ccr/IndexFollowingIT.java b/x-pack/plugin/ccr/src/test/java/org/elasticsearch/xpack/ccr/IndexFollowingIT.java
index a2d08c62d5bc0..89a5e8045c17e 100644
--- a/x-pack/plugin/ccr/src/test/java/org/elasticsearch/xpack/ccr/IndexFollowingIT.java
+++ b/x-pack/plugin/ccr/src/test/java/org/elasticsearch/xpack/ccr/IndexFollowingIT.java
@@ -761,13 +761,14 @@ public void testDeleteFollowerIndex() throws Exception {
             StatsResponses response = followerClient().execute(FollowStatsAction.INSTANCE, new StatsRequest()).actionGet();
             assertThat(response.getNodeFailures(), empty());
             assertThat(response.getTaskFailures(), empty());
-            assertThat(response.getStatsResponses(), hasSize(1));
-            assertThat(response.getStatsResponses().get(0).status().failedWriteRequests(), greaterThanOrEqualTo(1L));
-            ElasticsearchException fatalException = response.getStatsResponses().get(0).status().getFatalException();
-            assertThat(fatalException, notNullValue());
-            assertThat(fatalException.getMessage(), equalTo("no such index [index2]"));
+            if (response.getStatsResponses().isEmpty() == false) {
+                assertThat(response.getStatsResponses(), hasSize(1));
+                assertThat(response.getStatsResponses().get(0).status().failedWriteRequests(), greaterThanOrEqualTo(1L));
+                ElasticsearchException fatalException = response.getStatsResponses().get(0).status().getFatalException();
+                assertThat(fatalException, notNullValue());
+                assertThat(fatalException.getMessage(), equalTo("no such index [index2]"));
+            }
         });
-        pauseFollow("index2");
         ensureNoCcrTasks();
     }
 
@@ -1318,6 +1319,37 @@ public void testUpdateRemoteConfigsDuringFollowing() throws Exception {
         }
     }
 
+    public void testCleanUpShardFollowTasksForDeletedIndices() throws Exception {
+        final int numberOfShards = randomIntBetween(1, 10);
+        assertAcked(leaderClient().admin().indices().prepareCreate("index1")
+            .setSettings(Settings.builder()
+                .put(IndexSettings.INDEX_SOFT_DELETES_SETTING.getKey(), true)
+                .put(IndexMetaData.SETTING_NUMBER_OF_SHARDS, numberOfShards)
+                .put(IndexMetaData.SETTING_NUMBER_OF_REPLICAS, randomIntBetween(0, 1))
+                .build()));
+
+        final PutFollowAction.Request followRequest = putFollow("index1", "index2");
+        followerClient().execute(PutFollowAction.INSTANCE, followRequest).get();
+
+        leaderClient().prepareIndex("index1", "doc", "1").setSource("{}", XContentType.JSON).get();
+        assertBusy(() -> assertThat(followerClient().prepareSearch("index2").get().getHits().getTotalHits().value, equalTo(1L)));
+
+        assertBusy(() -> {
+            String action = ShardFollowTask.NAME + "[c]";
+            ListTasksResponse listTasksResponse = followerClient().admin().cluster().prepareListTasks().setActions(action).get();
+            assertThat(listTasksResponse.getTasks(), hasSize(numberOfShards));
+        });
+
+        assertAcked(followerClient().admin().indices().prepareDelete("index2"));
+
+        assertBusy(() -> {
+            String action = ShardFollowTask.NAME + "[c]";
+            ListTasksResponse listTasksResponse = followerClient().admin().cluster().prepareListTasks().setActions(action).get();
+            assertThat(listTasksResponse.getTasks(), hasSize(0));
+        });
+        ensureNoCcrTasks();
+    }
+
     private long getFollowTaskSettingsVersion(String followerIndex) {
         long settingsVersion = -1L;
         for (ShardFollowNodeTaskStatus status : getFollowTaskStatuses(followerIndex)) {