diff --git a/src/core/border_router/routing_manager.cpp b/src/core/border_router/routing_manager.cpp
index 761ae63ff..e5ffe1464 100644
--- a/src/core/border_router/routing_manager.cpp
+++ b/src/core/border_router/routing_manager.cpp
@@ -858,9 +858,11 @@ void RoutingManager::OnLinkPrefix::SetFrom(const PrefixTableEntry &aPrefixTableE
     mLastUpdateTime    = TimerMilli::GetNow();
 }
 
-bool RoutingManager::OnLinkPrefix::IsDeprecated(void) const
+bool RoutingManager::OnLinkPrefix::IsDeprecated(void) const { return GetDeprecationTime() <= TimerMilli::GetNow(); }
+
+TimeMilli RoutingManager::OnLinkPrefix::GetDeprecationTime(void) const
 {
-    return CalculateExpirationTime(mPreferredLifetime) <= TimerMilli::GetNow();
+    return CalculateExpirationTime(mPreferredLifetime);
 }
 
 TimeMilli RoutingManager::OnLinkPrefix::GetStaleTime(void) const
@@ -868,11 +870,6 @@ TimeMilli RoutingManager::OnLinkPrefix::GetStaleTime(void) const
     return CalculateExpirationTime(Min(kRtrAdvStaleTime, mPreferredLifetime));
 }
 
-TimeMilli RoutingManager::OnLinkPrefix::GetStaleTimeFromPreferredLifetime(void) const
-{
-    return CalculateExpirationTime(mPreferredLifetime);
-}
-
 void RoutingManager::OnLinkPrefix::AdoptValidAndPreferredLifetimesFrom(const OnLinkPrefix &aPrefix)
 {
     constexpr uint32_t kTwoHoursInSeconds = 2 * 3600;
@@ -3728,13 +3725,7 @@ void RoutingManager::PdPrefixManager::Process(const RouterAdvert::Icmp6Packet *a
 
     if (HasPrefix() && currentPrefixUpdated)
     {
-        // If the prefix is obtained from an RA message, use
-        // `GetStaleTime()` to apply the minimum `RA_STABLE_TIME`.
-        // Otherwise, calculate it directly from the prefix's
-        // preferred lifetime.
-
-        mTimer.FireAt((aPrefixTableEntry != nullptr) ? mPrefix.GetStaleTimeFromPreferredLifetime()
-                                                     : mPrefix.GetStaleTime());
+        mTimer.FireAt(mPrefix.GetDeprecationTime());
     }
     else
     {
diff --git a/src/core/border_router/routing_manager.hpp b/src/core/border_router/routing_manager.hpp
index 85f9cb944..f627f8be5 100644
--- a/src/core/border_router/routing_manager.hpp
+++ b/src/core/border_router/routing_manager.hpp
@@ -692,8 +692,8 @@ private:
         uint32_t  GetPreferredLifetime(void) const { return mPreferredLifetime; }
         void      ClearPreferredLifetime(void) { mPreferredLifetime = 0; }
         bool      IsDeprecated(void) const;
+        TimeMilli GetDeprecationTime(void) const;
         TimeMilli GetStaleTime(void) const;
-        TimeMilli GetStaleTimeFromPreferredLifetime(void) const;
         void      AdoptValidAndPreferredLifetimesFrom(const OnLinkPrefix &aPrefix);
         void      CopyInfoTo(PrefixTableEntry &aEntry, TimeMilli aNow) const;
 
diff --git a/tests/unit/test_routing_manager.cpp b/tests/unit/test_routing_manager.cpp
index b6040b7af..cf80ca3b3 100644
--- a/tests/unit/test_routing_manager.cpp
+++ b/tests/unit/test_routing_manager.cpp
@@ -3977,7 +3977,7 @@ void TestBorderRoutingProcessPlatfromGeneratedNd(void)
     }
 
     // 4. Short prefix will be extended to /64.
-    Log("Short prefix");
+    Log("4. Short prefix");
     {
         // The prefix will be padded to a /64 prefix.
         Ip6::Prefix raPrefix = PrefixFromString("2001:db8:cafe:0::", 64);
@@ -4004,6 +4004,31 @@ void TestBorderRoutingProcessPlatfromGeneratedNd(void)
         VerifyOmrPrefixInNetData(localOmr, /* aDefaultRoute */ false);
     }
 
+    // 5. Publish a prefix with long lifetime, and wait until it expired.
+    Log("5. RA message with long prefix lifetime");
+    {
+        Ip6::Prefix raPrefix = PrefixFromString("2001:db8:dead:beef::", 64);
+
+        SendRouterAdvertToBorderRoutingProcessIcmp6Ra({Pio(raPrefix, 5000, 5000)});
+
+        sExpectedRios.Add(raPrefix);
+        AdvanceTime(10 * 1000);
+
+        VerifyPdOmrPrefix(raPrefix);
+        VerifyOrQuit(sExpectedRios.SawAll());
+        VerifyOmrPrefixInNetData(raPrefix, /* aDefaultRoute */ false);
+
+        AdvanceTime(4900 * 1000);
+        sExpectedRios.Clear();
+        VerifyPdOmrPrefix(raPrefix);
+        VerifyOmrPrefixInNetData(raPrefix, /* aDefaultRoute */ false);
+
+        AdvanceTime(200 * 1000);
+        // Deprecated prefixes will be removed.
+        VerifyNoPdOmrPrefix();
+        VerifyOmrPrefixInNetData(localOmr, /* aDefaultRoute */ false);
+    }
+
     SuccessOrQuit(otBorderRoutingSetEnabled(sInstance, false));
     VerifyOrQuit(sHeapAllocatedPtrs.GetLength() <= heapAllocations);