diff --git a/ipykernel/control.py b/ipykernel/control.py
index 7ac56b7f9..4ba21dff5 100644
--- a/ipykernel/control.py
+++ b/ipykernel/control.py
@@ -15,7 +15,16 @@ def __init__(self, **kwargs):
         self.pydev_do_not_trace = True
         self.is_pydev_daemon_thread = True
 
-    def run(self): 
+    def run(self):
         self.io_loop.make_current()
-        self.io_loop.start()
-        self.io_loop.close(all_fds=True)
+        try:
+            self.io_loop.start()
+        finally:
+            self.io_loop.close()
+
+    def stop(self):
+        """Stop the thread.
+
+        This method is threadsafe.
+        """
+        self.io_loop.add_callback(self.io_loop.stop)
diff --git a/ipykernel/kernelapp.py b/ipykernel/kernelapp.py
index 9771c34dc..f43baf2c0 100644
--- a/ipykernel/kernelapp.py
+++ b/ipykernel/kernelapp.py
@@ -346,6 +346,10 @@ def close(self):
             self.log.debug("Closing iopub channel")
             self.iopub_thread.stop()
             self.iopub_thread.close()
+        if self.control_thread and self.control_thread.is_alive():
+            self.log.debug("Closing control thread")
+            self.control_thread.stop()
+            self.control_thread.join()
 
         if self.debugpy_socket and not self.debugpy_socket.closed:
             self.debugpy_socket.close()
@@ -487,7 +491,7 @@ def init_kernel(self):
                                 control_stream=control_stream,
                                 debugpy_stream=debugpy_stream,
                                 debug_shell_socket=self.debug_shell_socket,
-                                shell_stream=shell_stream, 
+                                shell_stream=shell_stream,
                                 control_thread=self.control_thread,
                                 iopub_thread=self.iopub_thread,
                                 iopub_socket=self.iopub_socket,