diff --git a/src/app/border_agent.cpp b/src/app/border_agent.cpp
index 164bb97db..5a819c3e9 100644
--- a/src/app/border_agent.cpp
+++ b/src/app/border_agent.cpp
@@ -28,6 +28,7 @@
 
 #include "border_agent.hpp"
 
+#include <atomic>
 #include <chrono>
 #include <thread>
 
@@ -42,6 +43,8 @@ namespace ot {
 
 namespace commissioner {
 
+static std::atomic<bool> gIsDiscoverCancelled;
+
 struct BorderAgentOrErrorMsg
 {
     BorderAgent mBorderAgent;
@@ -59,6 +62,11 @@ static int HandleRecord(const struct sockaddr *from,
                         size_t                 length,
                         void *                 user_data);
 
+void CancelDiscoverBorderAgent()
+{
+    gIsDiscoverCancelled = true;
+}
+
 Error DiscoverBorderAgent(BorderAgentHandler aBorderAgentHandler, size_t aTimeout)
 {
     static constexpr size_t             kDefaultBufferSize = 1024 * 16;
@@ -67,18 +75,21 @@ Error DiscoverBorderAgent(BorderAgentHandler aBorderAgentHandler, size_t aTimeou
 
     Error   error;
     uint8_t buf[kDefaultBufferSize];
+    size_t  borderAgentCount = 0;
 
     auto begin = std::chrono::system_clock::now();
 
     int socket = mdns_socket_open_ipv4();
     VerifyOrExit(socket >= 0, error = ERROR_IO_ERROR("failed to open mDNS IPv4 socket"));
 
+    gIsDiscoverCancelled = false;
+
     if (mdns_query_send(socket, kMdnsQueryType, kServiceName, strlen(kServiceName), buf, sizeof(buf)) != 0)
     {
         ExitNow(error = ERROR_IO_ERROR("failed to send mDNS query"));
     }
 
-    while (begin + std::chrono::milliseconds(aTimeout) >= std::chrono::system_clock::now())
+    while (!gIsDiscoverCancelled && begin + std::chrono::milliseconds(aTimeout) >= std::chrono::system_clock::now())
     {
         BorderAgentOrErrorMsg curBorderAgentOrErrorMsg;
 
@@ -91,11 +102,15 @@ Error DiscoverBorderAgent(BorderAgentHandler aBorderAgentHandler, size_t aTimeou
         else if (curBorderAgentOrErrorMsg.mBorderAgent.mPresentFlags != 0)
         {
             aBorderAgentHandler(&curBorderAgentOrErrorMsg.mBorderAgent, ERROR_NONE);
+            ++borderAgentCount;
         }
 
         std::this_thread::sleep_for(std::chrono::milliseconds(100));
     }
 
+    VerifyOrExit(!gIsDiscoverCancelled, error = ERROR_CANCELLED("Border Agent discovery was cancelled"));
+    VerifyOrExit(borderAgentCount != 0, error = ERROR_TIMEOUT("Found no Border Agent"));
+
 exit:
     if (socket >= 0)
     {
diff --git a/src/app/border_agent.hpp b/src/app/border_agent.hpp
index b2418d3af..555e4f30a 100644
--- a/src/app/border_agent.hpp
+++ b/src/app/border_agent.hpp
@@ -177,6 +177,14 @@ using BorderAgentHandler = std::function<void(const BorderAgent *aBorderAgent, c
  */
 Error DiscoverBorderAgent(BorderAgentHandler aBorderAgentHandler, size_t aTimeout);
 
+/**
+ * Cancel the call to DiscoverBorderAgent.
+ *
+ * This function is thread-safe.
+ *
+ */
+void CancelDiscoverBorderAgent();
+
 } // namespace commissioner
 
 } // namespace ot
diff --git a/src/app/cli/interpreter.cpp b/src/app/cli/interpreter.cpp
index 02bd01d5c..367108d3d 100644
--- a/src/app/cli/interpreter.cpp
+++ b/src/app/cli/interpreter.cpp
@@ -207,6 +207,8 @@ void Interpreter::CancelCommand()
     {
         mCommissioner->Stop();
     }
+
+    CancelDiscoverBorderAgent();
 }
 
 Interpreter::Expression Interpreter::Read()