Index: lld/trunk/ELF/LinkerScript.cpp
===================================================================
--- lld/trunk/ELF/LinkerScript.cpp
+++ lld/trunk/ELF/LinkerScript.cpp
@@ -751,6 +751,17 @@
   return nullptr;
 }
 
+static bool isHeaderSection(OutputSection *Sec) {
+  return Sec == Out::ElfHeader || Sec == Out::ProgramHeaders;
+}
+
+static OutputSection *findFirstSection(PhdrEntry *Load) {
+  for (OutputSection *Sec : OutputSections)
+    if (Sec->PtLoad == Load)
+      return Sec;
+  return nullptr;
+}
+
 // This function assigns offsets to input sections and an output section
 // for a single sections command (e.g. ".text { *(.text); }").
 void LinkerScript::assignOffsets(OutputSection *Sec) {
@@ -776,8 +787,12 @@
   // will set the LMA such that the difference between VMA and LMA for the
   // section is the same as the preceding output section in the same region
   // https://sourceware.org/binutils/docs-2.20/ld/Output-Section-LMA.html
+  // This, however, should only be done by the first "non-header" section
+  // in the segment.
   if (PhdrEntry *L = Ctx->OutSec->PtLoad)
-    L->LMAOffset = Ctx->LMAOffset;
+    if ((Sec == L->FirstSec) ||
+        (isHeaderSection(L->FirstSec) && (Sec == findFirstSection(L))))
+      L->LMAOffset = Ctx->LMAOffset;
 
   // We can call this method multiple times during the creation of
   // thunks and want to start over calculation each time.
@@ -954,13 +969,6 @@
   }
 }
 
-static OutputSection *findFirstSection(PhdrEntry *Load) {
-  for (OutputSection *Sec : OutputSections)
-    if (Sec->PtLoad == Load)
-      return Sec;
-  return nullptr;
-}
-
 static uint64_t computeBase(uint64_t Min, bool AllocateHeaders) {
   // If there is no SECTIONS or if the linkerscript is explicit about program
   // headers, do our best to allocate them.
Index: lld/trunk/test/ELF/linkerscript/Inputs/at8.s
===================================================================
--- lld/trunk/test/ELF/linkerscript/Inputs/at8.s
+++ lld/trunk/test/ELF/linkerscript/Inputs/at8.s
@@ -0,0 +1,8 @@
+.section .sec1,"aw",@progbits
+.quad   1
+
+.section .sec2,"aw",@progbits
+.quad   2
+
+.section .sec3,"aw",@progbits
+.quad   3
Index: lld/trunk/test/ELF/linkerscript/at8.test
===================================================================
--- lld/trunk/test/ELF/linkerscript/at8.test
+++ lld/trunk/test/ELF/linkerscript/at8.test
@@ -0,0 +1,31 @@
+# REQUIRES: x86
+# RUN: llvm-mc -filetype=obj -triple=x86_64-pc-linux %p/Inputs/at8.s -o %t.o
+# RUN: ld.lld %t.o --script %s -o %t
+# RUN: llvm-readelf -sections -program-headers %t | FileCheck %s
+
+MEMORY {
+  FLASH  : ORIGIN = 0x08000000, LENGTH = 0x100
+  RAM    : ORIGIN = 0x20000000, LENGTH = 0x200
+}
+
+SECTIONS {
+ .text : { *(.text) } > FLASH
+ .sec1 : { *(.sec1) } > RAM AT > FLASH
+ .sec2 : { *(.sec2) } > RAM
+ .sec3 : { *(.sec3) } > RAM AT > FLASH
+}
+
+# Make sure we do not issue a load-address overlap error
+# Previously, .sec3 would overwrite the LMAOffset in the
+# PT_LOAD header.
+
+# CHECK: Name              Type            Address          Off
+# CHECK: .text             PROGBITS        0000000008000000 001000
+# CHECK: .sec1             PROGBITS        0000000020000000 001000
+# CHECK: .sec2             PROGBITS        0000000020000008 001008
+# CHECK: .sec3             PROGBITS        0000000020000010 001010
+
+# CHECK: Program Headers:
+# CHECK:      Type  Offset   VirtAddr           PhysAddr
+# CHECK-NEXT: LOAD  0x001000 0x0000000020000000 0x0000000008000000
+# CHECK-NOT: LOAD