Index: ELF/LinkerScript.h
===================================================================
--- ELF/LinkerScript.h
+++ ELF/LinkerScript.h
@@ -228,6 +228,8 @@
 
   MemoryRegion *findMemoryRegion(OutputSectionCommand *Cmd, OutputSection *Sec);
 
+  void resetAddressState();
+
   void switchTo(OutputSection *Sec);
   void flush();
   void output(InputSection *Sec);
@@ -262,6 +264,8 @@
   void adjustSectionsBeforeSorting();
   void adjustSectionsAfterSorting();
 
+  void syncWithOS(OutputSection* OS);
+
   std::vector<PhdrEntry> createPhdrs();
   bool ignoreInterpSection();
 
Index: ELF/LinkerScript.cpp
===================================================================
--- ELF/LinkerScript.cpp
+++ ELF/LinkerScript.cpp
@@ -567,6 +567,21 @@
   return nullptr;
 }
 
+// Reset the members associated with address assigment to their initial values
+// this permits addressAssignment to be run again.
+void LinkerScript::resetAddressState() {
+  LMAOffset = 0;
+  CurOutSec = nullptr;
+  CurMemRegion = nullptr;
+  ThreadBssOffset = 0;
+  for (auto &MRI : Opt.MemoryRegions) {
+    MemoryRegion &MR = MRI.second;
+    MR.Offset = MR.Origin;
+  }
+  AlreadyOutputOS.clear();
+  AlreadyOutputIS.clear();
+}
+
 // This function assigns offsets to input sections and an output section
 // for a single sections command (e.g. ".text { *(.text); }").
 void LinkerScript::assignOffsets(OutputSectionCommand *Cmd) {
@@ -687,6 +702,80 @@
   removeEmptyCommands();
 }
 
+// Thunks are added to an OutputSection after InputSections are assigned to
+// InputSectionDescriptions. We need to resynchronize the OS->Sections and the
+// InputSectionDescriptions so that the Thunks are assigned the correct address
+//
+// The non-Thunk InputSections in OutputSection must match the order and
+// OutSecOff of their counterparts in the InputSectionDescriptions.
+void LinkerScript::syncWithOS(OutputSection *OS) {
+  // Find Commands associated with this OS
+  auto OutCmdPos = std::find_if(
+      Opt.Commands.begin(), Opt.Commands.end(),
+      [=](BaseCommand *Cmd) {
+        if (auto *OSCmd = dyn_cast<OutputSectionCommand>(Cmd))
+          return (OSCmd->Name == OS->Name);
+        return false;
+      });
+  if (OutCmdPos == Opt.Commands.end())
+    // LinkerScript does not describe the OS, no sync to do
+    return;
+
+  // To synchonize an InputSectionDescription we find the OutSecOff of the first
+  // InputSection in the next InputSectionDescription. We then transfer over
+  // all InputSections from OS->Section with a lower OutSecOff. This makes sure
+  // that Thunks added after the last InputSection in an InputSectionDescription
+  // get assigned to that the InputSectionDescription.
+  // ordered OS->Sections.
+
+  auto FindNextISDCmd =
+      [](std::vector<BaseCommand *>::iterator Begin,
+         std::vector<BaseCommand *>::iterator End) {
+        for (auto CmdIter = Begin; CmdIter != End; ++CmdIter) {
+          auto *Cmd = dyn_cast<InputSectionDescription>(*CmdIter);
+          if (Cmd && !Cmd->Sections.empty())
+            return CmdIter;
+        }
+        return End;
+      };
+  // Range to copy from OS->Sections
+  auto ISFromOSIter = OS->Sections.begin();
+  auto ISFromOSEnd = OS->Sections.end();
+
+  // Find first InputSectionDescription for this OS
+  auto *OutCmd = cast<OutputSectionCommand>(*OutCmdPos);
+  auto CmdIterEnd = OutCmd->Commands.end();
+  auto CmdIter = FindNextISDCmd(OutCmd->Commands.begin(), CmdIterEnd);
+
+  // Step through each InputSectionDescription, find the range
+  // [IsFromOsIter, ISFromOsEnd) to copy into it.
+  while (CmdIter != CmdIterEnd) {
+    auto NextCmdIter = FindNextISDCmd(CmdIter, CmdIterEnd);
+    if (NextCmdIter == CmdIterEnd)
+      // No more InputSectionDescriptions, we want all remaining InputSections
+      ISFromOSEnd = OS->Sections.end();
+    else {
+      // We have another InputSectionDescription for this OS, find the
+      // InputSection with OutSecOff >= the OutSecOff the first
+      // InputSection from the next InputSectionDescription to use as our
+      // limit.
+      auto *NextCmd = cast<InputSectionDescription>(*NextCmdIter);
+      auto NextIS = cast<InputSection>(NextCmd->Sections.front());
+      ISFromOSEnd = std::find_if(ISFromOSIter, OS->Sections.end(),
+                                 [NextIS](InputSection *IS) {
+                                   return IS->OutSecOff >= NextIS->OutSecOff;
+                                 });
+    }
+    // Copy range from OS->Sections to InputSectionDescription
+    std::vector<InputSectionBase *> Tmp;
+    for (; ISFromOSIter != ISFromOSEnd; ++ISFromOSIter)
+      Tmp.push_back(*ISFromOSIter);
+    auto *Cmd = cast<InputSectionDescription>(*CmdIter);
+    Cmd->Sections = std::move(Tmp);
+    CmdIter = NextCmdIter;
+  }
+}
+
 // When placing orphan sections, we want to place them after symbol assignments
 // so that an orphan after
 //   begin_foo = .;
@@ -789,6 +878,7 @@
 void LinkerScript::assignAddresses(std::vector<PhdrEntry> &Phdrs) {
   // Assign addresses as instructed by linker script SECTIONS sub-commands.
   Dot = 0;
+  resetAddressState();
   ErrorOnMissingSection = true;
   switchTo(Aether);
 
Index: ELF/Relocations.cpp
===================================================================
--- ELF/Relocations.cpp
+++ ELF/Relocations.cpp
@@ -43,6 +43,7 @@
 
 #include "Relocations.h"
 #include "Config.h"
+#include "LinkerScript.h"
 #include "Memory.h"
 #include "OutputSections.h"
 #include "Strings.h"
@@ -959,6 +960,11 @@
   std::merge(OS->Sections.begin(), OS->Sections.end(), Thunks.begin(),
              Thunks.end(), std::back_inserter(Tmp), MergeCmp);
   OS->Sections = std::move(Tmp);
+
+  // We need to insert the sections into the linker script input section
+  // commands for the correct output order
+  if (Script->Opt.HasSections)
+    Script->syncWithOS(OS);
   OS->assignOffsets();
 }
 
Index: ELF/Writer.cpp
===================================================================
--- ELF/Writer.cpp
+++ ELF/Writer.cpp
@@ -1176,6 +1176,15 @@
     // we need to assign addresses so that we can tell if jump instructions
     // are out of range. This will need to turn into a loop that converges
     // when no more Thunks are added
+    auto AddressesForThunks = [&]() {
+      if (Script->Opt.HasSections)
+        Script->assignAddresses(Phdrs);
+      else if (!Config->Relocatable) {
+        fixSectionAlignments();
+        assignAddresses();
+      }
+    };
+    AddressesForThunks();
     ThunkCreator<ELFT> TC;
     if (TC.createThunks(OutputSections))
       applySynthetic({In<ELFT>::MipsGot},
Index: test/ELF/mips-npic-call-pic-script.s
===================================================================
--- /dev/null
+++ test/ELF/mips-npic-call-pic-script.s
@@ -0,0 +1,141 @@
+# REQUIRES: mips
+# Check LA25 stubs creation. This stub code is necessary when
+# non-PIC code calls PIC function.
+# RUN: echo "SECTIONS { .out 0x20000 : { *(.text.*) . = . + 0x100 ;  *(.text) }  }" > %t1.script
+# RUN: llvm-mc -filetype=obj -triple=mips-unknown-linux \
+# RUN:   %p/Inputs/mips-fpic.s -o %t-fpic.o
+# RUN: llvm-mc -filetype=obj -triple=mips-unknown-linux \
+# RUN:   %p/Inputs/mips-fnpic.s -o %t-fnpic.o
+# RUN: ld.lld -r %t-fpic.o %t-fnpic.o -o %t-sto-pic.o
+# RUN: llvm-mc -filetype=obj -triple=mips-unknown-linux \
+# RUN:   %p/Inputs/mips-pic.s -o %t-pic.o
+# RUN: llvm-mc -filetype=obj -triple=mips-unknown-linux %s -o %t-npic.o
+# RUN: ld.lld --script %t1.script %t-npic.o %t-pic.o %t-sto-pic.o -o %t.exe --Map=m.txt
+# RUN: llvm-objdump -d %t.exe | FileCheck %s
+
+# CHECK: Disassembly of section .out:
+# CHECK-NEXT: __LA25Thunk_foo1a:
+# CHECK-NEXT:    20000:       3c 19 00 02     lui     $25, 2
+# CHECK-NEXT:    20004:       08 00 80 08     j       131104 <foo1a>
+# CHECK-NEXT:    20008:       27 39 00 20     addiu   $25, $25, 32
+# CHECK-NEXT:    2000c:       00 00 00 00     nop
+# CHECK: __LA25Thunk_foo1b:
+# CHECK-NEXT:    20010:       3c 19 00 02     lui     $25, 2
+# CHECK-NEXT:    20014:       08 00 80 09     j       131108 <foo1b>
+# CHECK-NEXT:    20018:       27 39 00 24     addiu   $25, $25, 36
+# CHECK-NEXT:    2001c:       00 00 00 00     nop
+# CHECK: foo1a:
+# CHECK-NEXT:    20020:       00 00 00 00     nop
+# CHECK: foo1b:
+# CHECK-NEXT:    20024:       00 00 00 00     nop
+# CHECK: __LA25Thunk_foo2:
+# CHECK-NEXT:    20028:       3c 19 00 02     lui     $25, 2
+# CHECK-NEXT:    2002c:       08 00 80 10     j       131136 <foo2>
+# CHECK-NEXT:    20030:       27 39 00 40     addiu   $25, $25, 64
+# CHECK-NEXT:    20034:       00 00 00 00     nop
+# CHECK-NEXT:    20038:       00 00 00 00     nop
+# CHECK-NEXT:    2003c:       00 00 00 00     nop
+# CHECK: foo2:
+# CHECK-NEXT:    20040:       00 00 00 00     nop
+# CHECK-NEXT:    20044:       00 00 00 00     nop
+# CHECK-NEXT:    20048:       00 00 00 00     nop
+# CHECK-NEXT:    2004c:       00 00 00 00     nop
+# CHECK-NEXT:    20050:       00 00 00 00     nop
+# CHECK-NEXT:    20054:       00 00 00 00     nop
+# CHECK-NEXT:    20058:       00 00 00 00     nop
+# CHECK-NEXT:    2005c:       00 00 00 00     nop
+# CHECK-NEXT:    20060:       00 00 00 00     nop
+# CHECK-NEXT:    20064:       00 00 00 00     nop
+# CHECK-NEXT:    20068:       00 00 00 00     nop
+# CHECK-NEXT:    2006c:       00 00 00 00     nop
+# CHECK-NEXT:    20070:       00 00 00 00     nop
+# CHECK-NEXT:    20074:       00 00 00 00     nop
+# CHECK-NEXT:    20078:       00 00 00 00     nop
+# CHECK-NEXT:    2007c:       00 00 00 00     nop
+# CHECK-NEXT:    20080:       00 00 00 00     nop
+# CHECK-NEXT:    20084:       00 00 00 00     nop
+# CHECK-NEXT:    20088:       00 00 00 00     nop
+# CHECK-NEXT:    2008c:       00 00 00 00     nop
+# CHECK-NEXT:    20090:       00 00 00 00     nop
+# CHECK-NEXT:    20094:       00 00 00 00     nop
+# CHECK-NEXT:    20098:       00 00 00 00     nop
+# CHECK-NEXT:    2009c:       00 00 00 00     nop
+# CHECK-NEXT:    200a0:       00 00 00 00     nop
+# CHECK-NEXT:    200a4:       00 00 00 00     nop
+# CHECK-NEXT:    200a8:       00 00 00 00     nop
+# CHECK-NEXT:    200ac:       00 00 00 00     nop
+# CHECK-NEXT:    200b0:       00 00 00 00     nop
+# CHECK-NEXT:    200b4:       00 00 00 00     nop
+# CHECK-NEXT:    200b8:       00 00 00 00     nop
+# CHECK-NEXT:    200bc:       00 00 00 00     nop
+# CHECK-NEXT:    200c0:       00 00 00 00     nop
+# CHECK-NEXT:    200c4:       00 00 00 00     nop
+# CHECK-NEXT:    200c8:       00 00 00 00     nop
+# CHECK-NEXT:    200cc:       00 00 00 00     nop
+# CHECK-NEXT:    200d0:       00 00 00 00     nop
+# CHECK-NEXT:    200d4:       00 00 00 00     nop
+# CHECK-NEXT:    200d8:       00 00 00 00     nop
+# CHECK-NEXT:    200dc:       00 00 00 00     nop
+# CHECK-NEXT:    200e0:       00 00 00 00     nop
+# CHECK-NEXT:    200e4:       00 00 00 00     nop
+# CHECK-NEXT:    200e8:       00 00 00 00     nop
+# CHECK-NEXT:    200ec:       00 00 00 00     nop
+# CHECK-NEXT:    200f0:       00 00 00 00     nop
+# CHECK-NEXT:    200f4:       00 00 00 00     nop
+# CHECK-NEXT:    200f8:       00 00 00 00     nop
+# CHECK-NEXT:    200fc:       00 00 00 00     nop
+# CHECK-NEXT:    20100:       00 00 00 00     nop
+# CHECK-NEXT:    20104:       00 00 00 00     nop
+# CHECK-NEXT:    20108:       00 00 00 00     nop
+# CHECK-NEXT:    2010c:       00 00 00 00     nop
+# CHECK-NEXT:    20110:       00 00 00 00     nop
+# CHECK-NEXT:    20114:       00 00 00 00     nop
+# CHECK-NEXT:    20118:       00 00 00 00     nop
+# CHECK-NEXT:    2011c:       00 00 00 00     nop
+# CHECK-NEXT:    20120:       00 00 00 00     nop
+# CHECK-NEXT:    20124:       00 00 00 00     nop
+# CHECK-NEXT:    20128:       00 00 00 00     nop
+# CHECK-NEXT:    2012c:       00 00 00 00     nop
+# CHECK-NEXT:    20130:       00 00 00 00     nop
+# CHECK-NEXT:    20134:       00 00 00 00     nop
+# CHECK-NEXT:    20138:       00 00 00 00     nop
+# CHECK-NEXT:    2013c:       00 00 00 00     nop
+# CHECK-NEXT:    20140:       00 00 00 00     nop
+# CHECK-NEXT:    20144:       00 00 00 00     nop
+# CHECK-NEXT:    20148:       00 00 00 00     nop
+# CHECK-NEXT:    2014c:       00 00 00 00     nop
+# CHECK: __start:
+# CHECK-NEXT:    20150:       0c 00 80 00     jal     131072 <__LA25Thunk_foo1a>
+# CHECK-NEXT:    20154:       00 00 00 00     nop
+# CHECK-NEXT:    20158:       0c 00 80 0a     jal     131112 <__LA25Thunk_foo2>
+# CHECK-NEXT:    2015c:       00 00 00 00     nop
+# CHECK-NEXT:    20160:       0c 00 80 04     jal     131088 <__LA25Thunk_foo1b>
+# CHECK-NEXT:    20164:       00 00 00 00     nop
+# CHECK-NEXT:    20168:       0c 00 80 0a     jal     131112 <__LA25Thunk_foo2>
+# CHECK-NEXT:    2016c:       00 00 00 00     nop
+# CHECK-NEXT:    20170:       0c 00 80 60     jal     131456 <__LA25Thunk_fpic>
+# CHECK-NEXT:    20174:       00 00 00 00     nop
+# CHECK-NEXT:    20178:       0c 00 80 68     jal     131488 <fnpic>
+# CHECK-NEXT:    2017c:       00 00 00 00     nop
+# CHECK: __LA25Thunk_fpic:
+# CHECK-NEXT:    20180:       3c 19 00 02     lui     $25, 2
+# CHECK-NEXT:    20184:       08 00 80 64     j       131472 <fpic>
+# CHECK-NEXT:    20188:       27 39 01 90     addiu   $25, $25, 400
+# CHECK-NEXT:    2018c:       00 00 00 00     nop
+# CHECK: fpic:
+# CHECK-NEXT:    20190:       00 00 00 00     nop
+# CHECK-NEXT:    20194:       00 00 00 00     nop
+# CHECK-NEXT:    20198:       00 00 00 00     nop
+# CHECK-NEXT:    2019c:       00 00 00 00     nop
+# CHECK: fnpic:
+# CHECK-NEXT:    201a0:       00 00 00 00     nop
+
+  .text
+  .globl __start
+__start:
+  jal foo1a
+  jal foo2
+  jal foo1b
+  jal foo2
+  jal fpic
+  jal fnpic