diff --git a/src/core/diags/README.md b/src/core/diags/README.md
index 9ec39c2cfed..b2fbd6f36a6 100644
--- a/src/core/diags/README.md
+++ b/src/core/diags/README.md
@@ -80,13 +80,14 @@ Done
 
 ### diag frame
 
-Usage: `diag frame [-c] [-p TX_POWER] [-s] <frame>`
+Usage: `diag frame [-c] [-p TX_POWER] [-s] [-u] <frame>`
 
 Set the frame (hex encoded) to be used by `diag send` and `diag repeat`. The frame may be overwritten by `diag send` and `diag repeat`.
 
-- Specify `-s` to indicate that tx security is already processed so that it should be skipped in the radio layer.
 - Specify `-c` to enable CSMA/CA for this frame in the radio layer.
 - Specify `-p` to specify the tx power in dBm for this frame.
+- Specify `-s` to indicate that tx security is already processed so that it should be skipped in the radio layer.
+- Specify `-u` to specify the `mInfo.mTxInfo.mIsHeaderUpdated` filed for this frame.
 
 ```bash
 > diag frame 11223344
diff --git a/src/core/diags/factory_diags.cpp b/src/core/diags/factory_diags.cpp
index ab88579f34d..6a42c7b619f 100644
--- a/src/core/diags/factory_diags.cpp
+++ b/src/core/diags/factory_diags.cpp
@@ -213,6 +213,7 @@ Diags::Diags(Instance &aInstance)
 
 void Diags::ResetTxPacket(void)
 {
+    mIsHeaderUpdated                               = false;
     mTxPacket->mInfo.mTxInfo.mTxDelayBaseTime      = 0;
     mTxPacket->mInfo.mTxInfo.mTxDelay              = 0;
     mTxPacket->mInfo.mTxInfo.mMaxCsmaBackoffs      = 0;
@@ -232,6 +233,7 @@ Error Diags::ProcessFrame(uint8_t aArgsLength, char *aArgs[])
     uint16_t size              = OT_RADIO_FRAME_MAX_SIZE;
     bool     securityProcessed = false;
     bool     csmaCaEnabled     = false;
+    bool     isHeaderUpdated   = false;
     int8_t   txPower           = OT_RADIO_POWER_INVALID;
 
     while (aArgsLength > 1)
@@ -239,6 +241,7 @@ Error Diags::ProcessFrame(uint8_t aArgsLength, char *aArgs[])
         if (StringMatch(aArgs[0], "-s"))
         {
             securityProcessed = true;
+            isHeaderUpdated   = true;
         }
         else if (StringMatch(aArgs[0], "-p"))
         {
@@ -255,6 +258,10 @@ Error Diags::ProcessFrame(uint8_t aArgsLength, char *aArgs[])
         {
             csmaCaEnabled = true;
         }
+        else if (StringMatch(aArgs[0], "-u"))
+        {
+            isHeaderUpdated = true;
+        }
         else
         {
             ExitNow(error = kErrorInvalidArgs);
@@ -276,6 +283,7 @@ Error Diags::ProcessFrame(uint8_t aArgsLength, char *aArgs[])
     mTxPacket->mInfo.mTxInfo.mTxPower             = txPower;
     mTxPacket->mLength                            = size;
     mIsTxPacketSet                                = true;
+    mIsHeaderUpdated                              = isHeaderUpdated;
 
 exit:
     AppendErrorResult(error);
@@ -514,7 +522,13 @@ void Diags::TransmitPacket(void)
 {
     mTxPacket->mChannel = mChannel;
 
-    if (!mIsTxPacketSet)
+    if (mIsTxPacketSet)
+    {
+        // The `mInfo.mTxInfo.mIsHeaderUpdated` field may be updated by the radio driver after the frame is sent,
+        // set the `mInfo.mTxInfo.mIsHeaderUpdated` field before transmitting the frame.
+        mTxPacket->mInfo.mTxInfo.mIsHeaderUpdated = mIsHeaderUpdated;
+    }
+    else
     {
         ResetTxPacket();
         mTxPacket->mLength = mTxLen;
diff --git a/src/core/diags/factory_diags.hpp b/src/core/diags/factory_diags.hpp
index a3f87042c2c..6d6ac6bc302 100644
--- a/src/core/diags/factory_diags.hpp
+++ b/src/core/diags/factory_diags.hpp
@@ -218,9 +218,10 @@ class Diags : public InstanceLocator, private NonCopyable
     uint8_t       mChannel;
     int8_t        mTxPower;
     uint8_t       mTxLen;
-    bool          mIsTxPacketSet;
-    bool          mRepeatActive;
-    bool          mDiagSendOn;
+    bool          mIsHeaderUpdated : 1;
+    bool          mIsTxPacketSet : 1;
+    bool          mRepeatActive : 1;
+    bool          mDiagSendOn : 1;
 #endif
 
     otDiagOutputCallback mOutputCallback;
diff --git a/src/lib/spinel/radio_spinel.cpp b/src/lib/spinel/radio_spinel.cpp
index 36b8dfb3f88..d7606ff6aff 100644
--- a/src/lib/spinel/radio_spinel.cpp
+++ b/src/lib/spinel/radio_spinel.cpp
@@ -1582,10 +1582,8 @@ void RadioSpinel::HandleTransmitDone(uint32_t          aCommand,
         error = SpinelStatusToOtError(status);
     }
 
-    static_cast<Mac::TxFrame *>(mTransmitFrame)->SetIsHeaderUpdated(headerUpdated);
-
-    if ((sRadioCaps & OT_RADIO_CAPS_TRANSMIT_SEC) && headerUpdated &&
-        static_cast<Mac::TxFrame *>(mTransmitFrame)->GetSecurityEnabled())
+    if ((sRadioCaps & OT_RADIO_CAPS_TRANSMIT_SEC) && (!mTransmitFrame->mInfo.mTxInfo.mIsHeaderUpdated) &&
+        headerUpdated && static_cast<Mac::TxFrame *>(mTransmitFrame)->GetSecurityEnabled())
     {
         uint8_t  keyId;
         uint32_t frameCounter;
@@ -1602,6 +1600,8 @@ void RadioSpinel::HandleTransmitDone(uint32_t          aCommand,
 #endif
     }
 
+    static_cast<Mac::TxFrame *>(mTransmitFrame)->SetIsHeaderUpdated(headerUpdated);
+
 exit:
     // A parse error indicates an RCP misbehavior, so recover the RCP immediately.
     mState = kStateTransmitDone;