diff --git a/src/core/common/message.hpp b/src/core/common/message.hpp
index 1448cdf70..344d938a9 100644
--- a/src/core/common/message.hpp
+++ b/src/core/common/message.hpp
@@ -52,6 +52,7 @@
 #include "common/locator.hpp"
 #include "common/non_copyable.hpp"
 #include "common/pool.hpp"
+#include "common/timer.hpp"
 #include "common/type_traits.hpp"
 #include "mac/mac_types.hpp"
 #include "thread/child_mask.hpp"
@@ -189,13 +190,13 @@ protected:
         MessagePool *mMessagePool; // Message pool for this message.
         void *       mQueue;       // The queue where message is queued (if any). Queue type from `mInPriorityQ`.
         uint32_t     mDatagramTag; // The datagram tag used for 6LoWPAN frags or IPv6fragmentation.
+        TimeMilli    mTimestamp;   // The message timestamp.
         uint16_t     mReserved;    // Number of reserved bytes (for header).
         uint16_t     mLength;      // Current message length (number of bytes).
         uint16_t     mOffset;      // A byte offset within the message.
         uint16_t     mMeshDest;    // Used for unicast non-link-local messages.
         uint16_t     mPanId;       // PAN ID (used for MLE Discover Request and Response).
         uint8_t      mChannel;     // The message channel (used for MLE Announce).
-        uint8_t      mTimeout;     // Seconds remaining before dropping the message.
         RssAverager  mRssAverager; // The averager maintaining the received signal strength (RSS) average.
 #if OPENTHREAD_CONFIG_MLE_LINK_METRICS_SUBJECT_ENABLE
         LqiAverager mLqiAverager; // The averager maintaining the Link quality indicator (LQI) average.
@@ -952,26 +953,26 @@ public:
     void SetChannel(uint8_t aChannel) { GetMetadata().mChannel = aChannel; }
 
     /**
-     * This method returns the timeout used for 6LoWPAN reassembly.
+     * This method returns the message timestamp.
      *
-     * @returns The time remaining in seconds.
+     * @returns The message timestamp.
      *
      */
-    uint8_t GetTimeout(void) const { return GetMetadata().mTimeout; }
+    TimeMilli GetTimestamp(void) const { return GetMetadata().mTimestamp; }
 
     /**
-     * This method sets the timeout used for 6LoWPAN reassembly.
+     * This method sets the message timestamp to a given time.
      *
-     * @param[in]  aTimeout  The timeout value.
+     * @param[in] aTimestamp   The timestamp value.
      *
      */
-    void SetTimeout(uint8_t aTimeout) { GetMetadata().mTimeout = aTimeout; }
+    void SetTimestamp(TimeMilli aTimestamp) { GetMetadata().mTimestamp = aTimestamp; }
 
     /**
-     * This method decrements the timeout.
+     * This method sets the message timestamp to the current time.
      *
      */
-    void DecrementTimeout(void) { GetMetadata().mTimeout--; }
+    void SetTimestampToNow(void) { SetTimestamp(TimerMilli::GetNow()); }
 
     /**
      * This method returns whether or not message forwarding is scheduled for direct transmission.
diff --git a/src/core/net/ip6.cpp b/src/core/net/ip6.cpp
index 0509eccad..ca8780c10 100644
--- a/src/core/net/ip6.cpp
+++ b/src/core/net/ip6.cpp
@@ -740,7 +740,7 @@ Error Ip6::HandleFragment(Message &aMessage, Netif *aNetif, MessageInfo &aMessag
         mReassemblyList.Enqueue(*message);
         SuccessOrExit(error = message->SetLength(aMessage.GetOffset()));
 
-        message->SetTimeout(kIp6ReassemblyTimeout);
+        message->SetTimestampToNow();
         message->SetOffset(0);
         message->SetDatagramTag(fragmentHeader.GetIdentification());
 
@@ -818,13 +818,11 @@ void Ip6::HandleTimeTick(void)
 
 void Ip6::UpdateReassemblyList(void)
 {
+    TimeMilli now = TimerMilli::GetNow();
+
     for (Message &message : mReassemblyList)
     {
-        if (message.GetTimeout() > 0)
-        {
-            message.DecrementTimeout();
-        }
-        else
+        if (now - message.GetTimestamp() >= TimeMilli::SecToMsec(kIp6ReassemblyTimeout))
         {
             LogNote("Reassembly timeout.");
             SendIcmpError(message, Icmp::Header::kTypeTimeExceeded, Icmp::Header::kCodeFragmReasTimeEx);
diff --git a/src/core/thread/mesh_forwarder.cpp b/src/core/thread/mesh_forwarder.cpp
index 9edf7eb2d..efc36516e 100644
--- a/src/core/thread/mesh_forwarder.cpp
+++ b/src/core/thread/mesh_forwarder.cpp
@@ -1266,7 +1266,7 @@ void MeshForwarder::HandleFragment(const uint8_t *       aFrame,
         SuccessOrExit(error);
 
         message->SetDatagramTag(fragmentHeader.GetDatagramTag());
-        message->SetTimeout(kReassemblyTimeout);
+        message->SetTimestampToNow();
         message->SetLinkInfo(aLinkInfo);
 
         VerifyOrExit(Get<Ip6::Filter>().Accept(*message), error = kErrorDrop);
@@ -1323,7 +1323,7 @@ void MeshForwarder::HandleFragment(const uint8_t *       aFrame,
 #if OPENTHREAD_CONFIG_MLE_LINK_METRICS_SUBJECT_ENABLE
         message->AddLqi(aLinkInfo.GetLqi());
 #endif
-        message->SetTimeout(kReassemblyTimeout);
+        message->SetTimestampToNow();
     }
 
 exit:
@@ -1377,13 +1377,11 @@ void MeshForwarder::HandleTimeTick(void)
 
 bool MeshForwarder::UpdateReassemblyList(void)
 {
+    TimeMilli now = TimerMilli::GetNow();
+
     for (Message &message : mReassemblyList)
     {
-        if (message.GetTimeout() > 0)
-        {
-            message.DecrementTimeout();
-        }
-        else
+        if (now - message.GetTimestamp() >= TimeMilli::SecToMsec(kReassemblyTimeout))
         {
             LogMessage(kMessageReassemblyDrop, message, kErrorReassemblyTimeout);