Index: COFF/Writer.cpp
===================================================================
--- COFF/Writer.cpp
+++ COFF/Writer.cpp
@@ -500,8 +500,8 @@
   createExportTable();
   mergeSections();
   readRelocTargets();
-  finalizeAddresses();
   removeEmptySections();
+  finalizeAddresses();
   setSectionPermissions();
   createSymbolAndStringTable();
 
@@ -885,7 +885,12 @@
 // The Windows loader doesn't seem to like empty sections,
 // so we remove them if any.
 void Writer::removeEmptySections() {
-  auto IsEmpty = [](OutputSection *S) { return S->getVirtualSize() == 0; };
+  auto IsEmpty = [](OutputSection *S) {
+    for (Chunk *C : S->Chunks)
+      if (C->getSize() > 0)
+        return false;
+    return true;
+  };
   OutputSections.erase(
       std::remove_if(OutputSections.begin(), OutputSections.end(), IsEmpty),
       OutputSections.end());
Index: test/COFF/header-size.s
===================================================================
--- /dev/null
+++ test/COFF/header-size.s
@@ -0,0 +1,12 @@
+// REQUIRES: x86
+// RUN: llvm-mc -filetype=obj -triple=x86_64-windows %s -o %t.obj
+// RUN: lld-link -entry:main -subsystem:console %t.obj -out:%t.exe
+// RUN: llvm-readobj -sections %t.exe | FileCheck %s
+    .globl main
+main:
+    ret
+
+// Check that the first section data comes at 512 bytes in the file.
+// If the size allocated for headers would include size for section
+// headers which aren't written, PointerToRawData would be 0x400 instead.
+// CHECK: PointerToRawData: 0x200