Index: ELF/Writer.cpp
===================================================================
--- ELF/Writer.cpp
+++ ELF/Writer.cpp
@@ -67,6 +67,7 @@
   void assignFileOffsets();
   void setPhdrs();
   void fixHeaders();
+  void fixHeaders(uintX_t BaseVA);
   void fixSectionAlignments();
   void fixAbsoluteSymbols();
   void openFile();
@@ -1129,8 +1130,7 @@
 // We should set file offsets and VAs for elf header and program headers
 // sections. These are special, we do not include them into output sections
 // list, but have them to simplify the code.
-template <class ELFT> void Writer<ELFT>::fixHeaders() {
-  uintX_t BaseVA = ScriptConfig->DoLayout ? 0 : Target->getVAStart();
+template <class ELFT> void Writer<ELFT>::fixHeaders(uintX_t BaseVA) {
   Out<ELFT>::ElfHeader->setVA(BaseVA);
   Out<ELFT>::ElfHeader->setFileOffset(0);
   uintX_t Off = Out<ELFT>::ElfHeader->getSize();
@@ -1138,6 +1138,11 @@
   Out<ELFT>::ProgramHeaders->setFileOffset(Off);
 }
 
+template <class ELFT> void Writer<ELFT>::fixHeaders() {
+  uintX_t BaseVA = ScriptConfig->DoLayout ? 0 : Target->getVAStart();
+  fixHeaders(BaseVA);
+}
+
 // Assign VAs (addresses at run-time) to output sections.
 template <class ELFT> void Writer<ELFT>::assignAddresses() {
   uintX_t VA = Target->getVAStart() + Out<ELFT>::ElfHeader->getSize() +
@@ -1186,6 +1191,18 @@
   uintX_t Off =
       Out<ELFT>::ElfHeader->getSize() + Out<ELFT>::ProgramHeaders->getSize();
 
+  if (ScriptConfig->DoLayout) {    
+    uintX_t BaseVA = Target->getVAStart();
+    if (!OutputSections.empty()) {      
+      // If we have any sections to output then calculate base VA, which
+      // should be page aligned
+      OutputSectionBase<ELFT> *First = OutputSections.front();         
+      BaseVA = alignDown(First->getVA() - Off, Target->PageSize);
+      Off = First->getVA() - BaseVA;
+    }
+    fixHeaders(BaseVA);
+  }
+  
   for (OutputSectionBase<ELFT> *Sec : OutputSections) {
     if (Sec->getType() == SHT_NOBITS) {
       Sec->setFileOffset(Off);
Index: test/ELF/linkerscript-phdr-check.s
===================================================================
--- test/ELF/linkerscript-phdr-check.s
+++ test/ELF/linkerscript-phdr-check.s
@@ -0,0 +1,16 @@
+# REQUIRES: x86
+# RUN: llvm-mc -filetype=obj -triple=x86_64-unknown-linux %s -o %t
+
+# RUN: echo "SECTIONS { . = 0x10000000; .text : {*(.text.*)} }" > %t.script
+# RUN: ld.lld -o %t1 --script %t.script %t
+# RUN: llvm-readobj -program-headers %t1 | FileCheck %s
+# CHECK:      ProgramHeaders [
+# CHECK-NEXT:  ProgramHeader {
+# CHECK-NEXT:    Type: PT_PHDR (0x6)
+# CHECK-NEXT:    Offset: 0x40
+# CHECK-NEXT:    VirtualAddress: 0xFFFF040
+
+.global _start
+_start:
+ nop
+