diff --git a/llvm/lib/Transforms/IPO/SampleProfile.cpp b/llvm/lib/Transforms/IPO/SampleProfile.cpp
--- a/llvm/lib/Transforms/IPO/SampleProfile.cpp
+++ b/llvm/lib/Transforms/IPO/SampleProfile.cpp
@@ -1106,16 +1106,26 @@
     }
 
     if (ProfileMergeInlinee) {
-      // Use entry samples as head samples during the merge, as inlinees
-      // don't have head samples.
-      assert(FS->getHeadSamples() == 0 && "Expect 0 head sample for inlinee");
-      const_cast<FunctionSamples *>(FS)->addHeadSamples(FS->getEntrySamples());
-
-      // Note that we have to do the merge right after processing function.
-      // This allows OutlineFS's profile to be used for annotation during
-      // top-down processing of functions' annotation.
-      FunctionSamples *OutlineFS = Reader->getOrCreateSamplesFor(*Callee);
-      OutlineFS->merge(*FS);
+      // A function call can be replicated by optimizations like callsite
+      // splitting or jump threading and the replicates end up sharing the
+      // sample nested callee profile instead of slicing the original inlinee's
+      // profile. We want to do merge exactly once by filtering out callee
+      // profiles with a non-zero head sample count.
+      if (FS->getHeadSamples() == 0) {
+        // Use entry samples as head samples during the merge, as inlinees
+        // don't have head samples.
+        const_cast<FunctionSamples *>(FS)->addHeadSamples(
+            FS->getEntrySamples());
+
+        // Note that we have to do the merge right after processing function.
+        // This allows OutlineFS's profile to be used for annotation during
+        // top-down processing of functions' annotation.
+        FunctionSamples *OutlineFS = Reader->getOrCreateSamplesFor(*Callee);
+        OutlineFS->merge(*FS);
+      } else
+        assert(FS->getHeadSamples() == FS->getEntrySamples() &&
+               "Expect same head and entry sample counts for profiles already "
+               "merged.");
     } else {
       auto pair =
           notInlinedCallInfo.try_emplace(Callee, NotInlinedProfileInfo{0});
diff --git a/llvm/test/Transforms/SampleProfile/inline-mergeprof-dup.ll b/llvm/test/Transforms/SampleProfile/inline-mergeprof-dup.ll
new file mode 100644
--- /dev/null
+++ b/llvm/test/Transforms/SampleProfile/inline-mergeprof-dup.ll
@@ -0,0 +1,80 @@
+;; Test we merge non-inlined profile only once with '-sample-profile-merge-inlinee'
+; RUN: opt < %s -passes='function(callsite-splitting),sample-profile' -sample-profile-file=%S/Inputs/inline-mergeprof.prof -sample-profile-merge-inlinee=true -S | FileCheck %s
+
+%struct.bitmap = type { i32, %struct.bitmap* }
+
+; CHECK-LABEL: @main
+define void @main(i1 %c, %struct.bitmap* %a_elt, %struct.bitmap* %b_elt) #0 !dbg !6 {
+entry:
+  br label %Top
+
+Top:
+  %tobool1 = icmp eq %struct.bitmap* %a_elt, null
+  br i1 %tobool1, label %CallSiteBB, label %NextCond
+
+NextCond:
+  %cmp = icmp ne %struct.bitmap* %b_elt, null
+  br i1 %cmp, label %CallSiteBB, label %End
+
+CallSiteBB:
+  %p = phi i1 [0, %Top], [%c, %NextCond]
+;; The call site is replicated by callsite-splitting pass and they end up share the same sample profile
+; CHECK: call void @_Z3sumii(%struct.bitmap* null, %struct.bitmap* null, %struct.bitmap* %b_elt, i1 false)
+; CHECK: call void @_Z3sumii(%struct.bitmap* nonnull %a_elt, %struct.bitmap* nonnull %a_elt, %struct.bitmap* nonnull %b_elt, i1 %c)
+  call void @_Z3sumii(%struct.bitmap* %a_elt, %struct.bitmap* %a_elt, %struct.bitmap* %b_elt, i1 %p), !dbg !8
+  br label %End
+
+End:
+  ret void
+}
+
+define void @_Z3sumii(%struct.bitmap* %dst_elt, %struct.bitmap* %a_elt, %struct.bitmap* %b_elt, i1 %c)  #0 !dbg !12 {
+entry:
+  %tobool = icmp ne %struct.bitmap* %a_elt, null
+  %tobool1 = icmp ne %struct.bitmap* %b_elt, null
+  %or.cond = and i1 %tobool, %tobool1, !dbg !13
+  br i1 %or.cond, label %Cond, label %Big
+
+Cond:
+  %cmp = icmp eq %struct.bitmap*  %dst_elt, %a_elt, !dbg !14
+  br i1 %cmp, label %Small, label %Big, !dbg !15
+
+Small:
+  br label %End
+
+Big:
+  br label %End
+
+End:
+  ret void
+}
+
+attributes #0 = { "use-sample-profile" }
+
+!llvm.dbg.cu = !{!0}
+!llvm.module.flags = !{!3, !4}
+!llvm.ident = !{!5}
+
+!0 = distinct !DICompileUnit(language: DW_LANG_C_plus_plus, file: !1, producer: "clang version 3.5 ", isOptimized: false, runtimeVersion: 0, emissionKind: NoDebug, enums: !2, retainedTypes: !2, globals: !2, imports: !2)
+!1 = !DIFile(filename: "calls.cc", directory: ".")
+!2 = !{}
+!3 = !{i32 2, !"Dwarf Version", i32 4}
+!4 = !{i32 1, !"Debug Info Version", i32 3}
+!5 = !{!"clang version 3.5 "}
+!6 = distinct !DISubprogram(name: "main", scope: !1, file: !1, line: 7, type: !7, scopeLine: 7, virtualIndex: 6, flags: DIFlagPrototyped, spFlags: DISPFlagDefinition, unit: !0, retainedNodes: !2)
+!7 = !DISubroutineType(types: !2)
+!8 = !DILocation(line: 10, scope: !9)
+!9 = !DILexicalBlockFile(scope: !10, file: !1, discriminator: 2)
+!10 = distinct !DILexicalBlock(scope: !6, file: !1, line: 10)
+!11 = !DILocation(line: 12, scope: !6)
+!12 = distinct !DISubprogram(name: "sum", scope: !1, file: !1, line: 3, type: !7, scopeLine: 3, virtualIndex: 6, flags: DIFlagPrototyped, spFlags: DISPFlagDefinition, unit: !0, retainedNodes: !2)
+!13 = !DILocation(line: 4, scope: !12)
+!14 = !DILocation(line: 5, scope: !12)
+!15 = !DILocation(line: 6, scope: !12)
+
+
+;; Check the profile of funciton sum is only merged once though the original callsite is replicted.
+; CHECK: name: "sum"
+; CHECK-NEXT: {!"function_entry_count", i64 46}
+; CHECK: !{!"branch_weights", i32 11, i32 37}
+; CHECK: !{!"branch_weights", i32 11, i32 1}