diff --git a/src/core/mac/sub_mac.cpp b/src/core/mac/sub_mac.cpp
index 5334f62e6..d3f248b00 100644
--- a/src/core/mac/sub_mac.cpp
+++ b/src/core/mac/sub_mac.cpp
@@ -279,7 +279,7 @@ void SubMac::HandleReceiveDone(RxFrame *aFrame, Error aError)
 
     if (!ShouldHandleTransmitSecurity() && aFrame != nullptr && aFrame->mInfo.mRxInfo.mAckedWithSecEnhAck)
     {
-        UpdateFrameCounter(aFrame->mInfo.mRxInfo.mAckFrameCounter);
+        SignalFrameCounterUsed(aFrame->mInfo.mRxInfo.mAckFrameCounter);
     }
 
 #if OPENTHREAD_CONFIG_MAC_CSL_RECEIVER_ENABLE
@@ -362,7 +362,7 @@ void SubMac::ProcessTransmitSecurity(void)
         uint32_t frameCounter = GetFrameCounter();
 
         mTransmitFrame.SetFrameCounter(frameCounter);
-        UpdateFrameCounter(frameCounter + 1);
+        SignalFrameCounterUsed(frameCounter);
     }
 
     extAddress = &GetExtAddress();
@@ -536,7 +536,7 @@ void SubMac::HandleTransmitDone(TxFrame &aFrame, RxFrame *aAckFrame, Error aErro
         OT_UNREACHABLE_CODE(ExitNow());
     }
 
-    UpdateFrameCounterOnTxDone(aFrame);
+    SignalFrameCounterUsedOnTxDone(aFrame);
 
     // Determine whether a CSMA retry is required.
 
@@ -571,7 +571,7 @@ exit:
     return;
 }
 
-void SubMac::UpdateFrameCounterOnTxDone(const TxFrame &aFrame)
+void SubMac::SignalFrameCounterUsedOnTxDone(const TxFrame &aFrame)
 {
     uint8_t  keyIdMode;
     uint32_t frameCounter;
@@ -598,7 +598,7 @@ void SubMac::UpdateFrameCounterOnTxDone(const TxFrame &aFrame)
     VerifyOrExit(keyIdMode == Frame::kKeyIdMode1);
 
     VerifyOrExit(aFrame.GetFrameCounter(frameCounter) == kErrorNone, OT_ASSERT(allowError));
-    UpdateFrameCounter(frameCounter);
+    SignalFrameCounterUsed(frameCounter);
 
 exit:
     return;
@@ -876,11 +876,23 @@ exit:
     return;
 }
 
-void SubMac::UpdateFrameCounter(uint32_t aFrameCounter)
+void SubMac::SignalFrameCounterUsed(uint32_t aFrameCounter)
 {
-    mFrameCounter = aFrameCounter;
+    mCallbacks.FrameCounterUsed(aFrameCounter);
 
-    mCallbacks.FrameCounterUpdated(aFrameCounter);
+    // It not always guaranteed that this method is invoked in order
+    // for different counter values (i.e., we may get it for a
+    // smaller counter value after a lager one). This may happen due
+    // to a new counter value being used for an enhanced-ack during
+    // tx of a frame. Note that the newer counter used for enhanced-ack
+    // is processed from `HandleReceiveDone()` which can happen before
+    // processing of the older counter value from `HandleTransmitDone()`.
+
+    VerifyOrExit(mFrameCounter <= aFrameCounter);
+    mFrameCounter = aFrameCounter + 1;
+
+exit:
+    return;
 }
 
 void SubMac::SetFrameCounter(uint32_t aFrameCounter)
diff --git a/src/core/mac/sub_mac.hpp b/src/core/mac/sub_mac.hpp
index 9281e6fdb..64b7a3aa3 100644
--- a/src/core/mac/sub_mac.hpp
+++ b/src/core/mac/sub_mac.hpp
@@ -195,12 +195,15 @@ public:
         void EnergyScanDone(int8_t aMaxRssi);
 
         /**
-         * This method notifies user of `SubMac` that MAC frame counter is updated.
+         * This method notifies user of `SubMac` that a specific MAC frame counter is used for transmission.
          *
-         * @param[in]  aFrameCounter  The MAC frame counter value.
+         * It is possible that this callback is invoked out of order in terms of counter values (i.e., called for a
+         * smaller counter value after a call for a larger counter value).
+         *
+         * @param[in]  aFrameCounter  The MAC frame counter value which was used.
          *
          */
-        void FrameCounterUpdated(uint32_t aFrameCounter);
+        void FrameCounterUsed(uint32_t aFrameCounter);
     };
 
     /**
@@ -622,7 +625,7 @@ private:
     bool ShouldHandleTransmitTargetTime(void) const;
 
     void ProcessTransmitSecurity(void);
-    void UpdateFrameCounter(uint32_t aFrameCounter);
+    void SignalFrameCounterUsed(uint32_t aFrameCounter);
     void StartCsmaBackoff(void);
     void BeginTransmit(void);
     void SampleRssi(void);
@@ -630,7 +633,7 @@ private:
     void HandleReceiveDone(RxFrame *aFrame, Error aError);
     void HandleTransmitStarted(TxFrame &aFrame);
     void HandleTransmitDone(TxFrame &aFrame, RxFrame *aAckFrame, Error aError);
-    void UpdateFrameCounterOnTxDone(const TxFrame &aFrame);
+    void SignalFrameCounterUsedOnTxDone(const TxFrame &aFrame);
     void HandleEnergyScanDone(int8_t aMaxRssi);
 
     static void HandleTimer(Timer &aTimer);
diff --git a/src/core/mac/sub_mac_callbacks.cpp b/src/core/mac/sub_mac_callbacks.cpp
index 35bb64ddc..b61ad283f 100644
--- a/src/core/mac/sub_mac_callbacks.cpp
+++ b/src/core/mac/sub_mac_callbacks.cpp
@@ -107,9 +107,9 @@ void SubMac::Callbacks::EnergyScanDone(int8_t aMaxRssi)
     }
 }
 
-void SubMac::Callbacks::FrameCounterUpdated(uint32_t aFrameCounter)
+void SubMac::Callbacks::FrameCounterUsed(uint32_t aFrameCounter)
 {
-    Get<KeyManager>().MacFrameCounterUpdated(aFrameCounter);
+    Get<KeyManager>().MacFrameCounterUsed(aFrameCounter);
 }
 
 #elif OPENTHREAD_RADIO
@@ -142,7 +142,7 @@ void SubMac::Callbacks::EnergyScanDone(int8_t aMaxRssi)
     Get<LinkRaw>().InvokeEnergyScanDone(aMaxRssi);
 }
 
-void SubMac::Callbacks::FrameCounterUpdated(uint32_t aFrameCounter)
+void SubMac::Callbacks::FrameCounterUsed(uint32_t aFrameCounter)
 {
     OT_UNUSED_VARIABLE(aFrameCounter);
 }
diff --git a/src/core/thread/key_manager.cpp b/src/core/thread/key_manager.cpp
index 6d9a7d850..7ac5bfbdf 100644
--- a/src/core/thread/key_manager.cpp
+++ b/src/core/thread/key_manager.cpp
@@ -429,17 +429,26 @@ void KeyManager::SetAllMacFrameCounters(uint32_t aMacFrameCounter)
 }
 
 #if OPENTHREAD_CONFIG_RADIO_LINK_IEEE_802_15_4_ENABLE
-void KeyManager::MacFrameCounterUpdated(uint32_t aMacFrameCounter)
+void KeyManager::MacFrameCounterUsed(uint32_t aMacFrameCounter)
 {
-    mMacFrameCounters.Set154(aMacFrameCounter);
+    // This is callback from `SubMac` to indicate that a frame
+    // counter value is used for tx. We ensure to handle it
+    // even if it is called out of order.
+
+    VerifyOrExit(mMacFrameCounters.Get154() <= aMacFrameCounter);
+
+    mMacFrameCounters.Set154(aMacFrameCounter + 1);
 
     if (mMacFrameCounters.Get154() >= mStoredMacFrameCounter)
     {
         IgnoreError(Get<Mle::MleRouter>().Store());
     }
+
+exit:
+    return;
 }
 #else
-void KeyManager::MacFrameCounterUpdated(uint32_t)
+void KeyManager::MacFrameCounterUsed(uint32_t)
 {
 }
 #endif
diff --git a/src/core/thread/key_manager.hpp b/src/core/thread/key_manager.hpp
index 407eab023..c1b77f553 100644
--- a/src/core/thread/key_manager.hpp
+++ b/src/core/thread/key_manager.hpp
@@ -541,12 +541,14 @@ public:
     void UpdateKeyMaterial(void);
 
     /**
-     * This method handles MAC frame counter change (callback from `SubMac` for 15.4 security frame change)
+     * This method handles MAC frame counter changes (callback from `SubMac` for 15.4 security frame change).
+     *
+     * This is called to indicate the @p aMacFrameCounter value is now used.
      *
      * @param[in]  aMacFrameCounter  The 15.4 link MAC frame counter value.
      *
      */
-    void MacFrameCounterUpdated(uint32_t aMacFrameCounter);
+    void MacFrameCounterUsed(uint32_t aMacFrameCounter);
 
 private:
     static constexpr uint32_t kDefaultKeySwitchGuardTime = 624;