diff --git a/src/core/api/thread_api.cpp b/src/core/api/thread_api.cpp
index 97e5508f0..b5661df64 100644
--- a/src/core/api/thread_api.cpp
+++ b/src/core/api/thread_api.cpp
@@ -275,7 +275,8 @@ uint32_t otThreadGetKeySequenceCounter(otInstance *aInstance)
 
 void otThreadSetKeySequenceCounter(otInstance *aInstance, uint32_t aKeySequenceCounter)
 {
-    AsCoreType(aInstance).Get<KeyManager>().SetCurrentKeySequence(aKeySequenceCounter, KeyManager::kForceUpdate);
+    AsCoreType(aInstance).Get<KeyManager>().SetCurrentKeySequence(
+        aKeySequenceCounter, KeyManager::kForceUpdate | KeyManager::kGuardTimerUnchanged);
 }
 
 uint16_t otThreadGetKeySwitchGuardTime(otInstance *aInstance)
diff --git a/src/core/mac/mac.cpp b/src/core/mac/mac.cpp
index 9ca72fdba..d1fbd0a8e 100644
--- a/src/core/mac/mac.cpp
+++ b/src/core/mac/mac.cpp
@@ -1641,7 +1641,7 @@ Error Mac::ProcessReceiveSecurity(RxFrame &aFrame, const Address &aSrcAddr, Neig
 
         if (keySequence > keyManager.GetCurrentKeySequence())
         {
-            keyManager.SetCurrentKeySequence(keySequence, KeyManager::kApplyKeySwitchGuard);
+            keyManager.SetCurrentKeySequence(keySequence, KeyManager::kApplySwitchGuard | KeyManager::kResetGuardTimer);
         }
     }
 
diff --git a/src/core/thread/key_manager.cpp b/src/core/thread/key_manager.cpp
index d38fdb8b5..9f40c9ec2 100644
--- a/src/core/thread/key_manager.cpp
+++ b/src/core/thread/key_manager.cpp
@@ -368,11 +368,11 @@ void KeyManager::UpdateKeyMaterial(void)
 #endif
 }
 
-void KeyManager::SetCurrentKeySequence(uint32_t aKeySequence, KeySequenceUpdateMode aUpdateMode)
+void KeyManager::SetCurrentKeySequence(uint32_t aKeySequence, KeySeqUpdateFlags aFlags)
 {
     VerifyOrExit(aKeySequence != mKeySequence, Get<Notifier>().SignalIfFirst(kEventThreadKeySeqCounterChanged));
 
-    if (aUpdateMode == kApplyKeySwitchGuard)
+    if (aFlags & kApplySwitchGuard)
     {
         VerifyOrExit(mKeySwitchGuardTimer == 0);
     }
@@ -384,7 +384,11 @@ void KeyManager::SetCurrentKeySequence(uint32_t aKeySequence, KeySequenceUpdateM
     mMleFrameCounter = 0;
 
     ResetKeyRotationTimer();
-    mKeySwitchGuardTimer = mKeySwitchGuardTime;
+
+    if (aFlags & kResetGuardTimer)
+    {
+        mKeySwitchGuardTimer = mKeySwitchGuardTime;
+    }
 
     Get<Notifier>().Signal(kEventThreadKeySeqCounterChanged);
 
@@ -528,7 +532,7 @@ void KeyManager::CheckForKeyRotation(void)
 {
     if (mHoursSinceKeyRotation >= mSecurityPolicy.mRotationTime)
     {
-        SetCurrentKeySequence(mKeySequence + 1, kForceUpdate);
+        SetCurrentKeySequence(mKeySequence + 1, kForceUpdate | kResetGuardTimer);
     }
 }
 
diff --git a/src/core/thread/key_manager.hpp b/src/core/thread/key_manager.hpp
index 099854c45..56a64acb3 100644
--- a/src/core/thread/key_manager.hpp
+++ b/src/core/thread/key_manager.hpp
@@ -221,16 +221,24 @@ class KeyManager : public InstanceLocator, private NonCopyable
 {
 public:
     /**
-     * Determines whether to apply or ignore key switch guard when updating the key sequence.
+     * Defines bit-flag constants specifying how to handle key sequence update used in `KeySeqUpdateFlags`.
+     *
+     */
+    enum KeySeqUpdateFlag : uint8_t
+    {
+        kApplySwitchGuard    = (1 << 0), ///< Apply key switch guard check.
+        kForceUpdate         = (0 << 0), ///< Ignore key switch guard check and forcibly update.
+        kResetGuardTimer     = (1 << 1), ///< On key seq change, reset the guard timer.
+        kGuardTimerUnchanged = (0 << 1), ///< On key seq change, leave guard timer unchanged.
+    };
+
+    /**
+     * Represents a combination of `KeySeqUpdateFlag` bits.
      *
      * Used as input by `SetCurrentKeySequence()`.
      *
      */
-    enum KeySequenceUpdateMode : uint8_t
-    {
-        kApplyKeySwitchGuard, ///< Apply key switch guard check before setting the new key sequence.
-        kForceUpdate,         ///< Ignore key switch guard check and forcibly update the key sequence to new value.
-    };
+    typedef uint8_t KeySeqUpdateFlags;
 
     /**
      * Initializes the object.
@@ -342,14 +350,12 @@ public:
     /**
      * Sets the current key sequence value.
      *
-     * If @p aMode is `kApplyKeySwitchGuard`, the current key switch guard timer is checked and only if it is zero, key
-     * sequence will be updated.
-     *
      * @param[in]  aKeySequence    The key sequence value.
-     * @param[in]  aUpdateMode     Whether or not to apply the key switch guard.
+     * @param[in]  aFlags          Specify behavior when updating the key sequence, i.e., whether or not to apply the
+     *                             key switch guard or reset guard timer upon change.
      *
      */
-    void SetCurrentKeySequence(uint32_t aKeySequence, KeySequenceUpdateMode aUpdateMode);
+    void SetCurrentKeySequence(uint32_t aKeySequence, KeySeqUpdateFlags aFlags);
 
 #if OPENTHREAD_CONFIG_RADIO_LINK_TREL_ENABLE
     /**
diff --git a/src/core/thread/mle.cpp b/src/core/thread/mle.cpp
index b45d07529..76a397fdd 100644
--- a/src/core/thread/mle.cpp
+++ b/src/core/thread/mle.cpp
@@ -371,7 +371,8 @@ void Mle::Restore(void)
 
     SuccessOrExit(Get<Settings>().Read(networkInfo));
 
-    Get<KeyManager>().SetCurrentKeySequence(networkInfo.GetKeySequence(), KeyManager::kForceUpdate);
+    Get<KeyManager>().SetCurrentKeySequence(networkInfo.GetKeySequence(),
+                                            KeyManager::kForceUpdate | KeyManager::kGuardTimerUnchanged);
     Get<KeyManager>().SetMleFrameCounter(networkInfo.GetMleFrameCounter());
     Get<KeyManager>().SetAllMacFrameCounters(networkInfo.GetMacFrameCounter(), /* aSetIfLarger */ false);
 
@@ -2721,33 +2722,43 @@ void Mle::ProcessKeySequence(RxInfo &aRxInfo)
     //                    neighbor.
     //                 Otherwise larger key seq MUST NOT be adopted.
 
+    bool                          isNextKeySeq;
+    KeyManager::KeySeqUpdateFlags flags = 0;
+
     VerifyOrExit(aRxInfo.mKeySequence > Get<KeyManager>().GetCurrentKeySequence());
 
+    isNextKeySeq = (aRxInfo.mKeySequence - Get<KeyManager>().GetCurrentKeySequence() == 1);
+
     switch (aRxInfo.mClass)
     {
     case RxInfo::kAuthoritativeMessage:
-        Get<KeyManager>().SetCurrentKeySequence(aRxInfo.mKeySequence, KeyManager::kForceUpdate);
+        flags = KeyManager::kForceUpdate;
         break;
 
     case RxInfo::kPeerMessage:
-        if ((aRxInfo.mNeighbor != nullptr) && aRxInfo.mNeighbor->IsStateValid())
+        VerifyOrExit(aRxInfo.IsNeighborStateValid());
+
+        if (!isNextKeySeq)
         {
-            if (aRxInfo.mKeySequence - Get<KeyManager>().GetCurrentKeySequence() == 1)
-            {
-                Get<KeyManager>().SetCurrentKeySequence(aRxInfo.mKeySequence, KeyManager::kApplyKeySwitchGuard);
-            }
-            else
-            {
-                LogInfo("Large key seq jump in peer class msg from 0x%04x ", aRxInfo.mNeighbor->GetRloc16());
-                ReestablishLinkWithNeighbor(*aRxInfo.mNeighbor);
-            }
+            LogInfo("Large key seq jump in peer class msg from 0x%04x ", aRxInfo.mNeighbor->GetRloc16());
+            ReestablishLinkWithNeighbor(*aRxInfo.mNeighbor);
+            ExitNow();
         }
+
+        flags = KeyManager::kApplySwitchGuard;
         break;
 
     case RxInfo::kUnknown:
-        break;
+        ExitNow();
     }
 
+    if (isNextKeySeq)
+    {
+        flags |= KeyManager::kResetGuardTimer;
+    }
+
+    Get<KeyManager>().SetCurrentKeySequence(aRxInfo.mKeySequence, flags);
+
 exit:
     return;
 }