Index: test/tools/llvm-objcopy/marker-segment.test
===================================================================
--- test/tools/llvm-objcopy/marker-segment.test
+++ test/tools/llvm-objcopy/marker-segment.test
@@ -0,0 +1,86 @@
+# RUN: yaml2obj %s -o %t
+# RUN: llvm-objcopy %t %t2
+# RUN: llvm-readobj -program-headers %t2 | FileCheck %s
+
+!ELF
+FileHeader:
+  Class:           ELFCLASS32
+  Data:            ELFDATA2LSB
+  Type:            ET_EXEC
+  Machine:         EM_ARM
+Sections:
+  - Name:            .text
+    Type:            SHT_PROGBITS
+    Flags:           [ SHF_ALLOC, SHF_EXECINSTR ]
+    Address:         0x1000
+    AddressAlign:    0x0000000000001000
+    Content:         "FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF"
+  - Name:            .data
+    Type:            SHT_PROGBITS
+    Flags:           [ SHF_ALLOC ]
+    Address:         0x2000
+    AddressAlign:    0x0000000000001000
+    Content:         "FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF"
+ProgramHeaders:
+  - Type: PT_LOAD
+    Flags: [ PF_X, PF_R ]
+    VAddr: 0x1000
+    PAddr: 0x1000
+    Align: 0x1000
+    Sections:
+      - Section: .text
+  - Type: PT_LOAD
+    Flags: [ PF_R, PF_W ]
+    VAddr: 0x2000
+    PAddr: 0x2000
+    Align: 0x1000
+    Sections:
+      - Section: .data
+  - Type: 0x6474e551 # GNU_STACK
+    Flags: [ PF_R, PF_W ]
+    VAddr: 0x0000
+    PAddr: 0x0000
+    Align: 0x0000
+
+
+#CHECK:     ProgramHeaders [
+#CHECK-NEXT:   ProgramHeader {
+#CHECK-NEXT:    Type: PT_LOAD
+#CHECK-NEXT:    Offset: 0x1000
+#CHECK-NEXT:    VirtualAddress: 0x1000
+#CHECK-NEXT:    PhysicalAddress: 0x1000
+#CHECK-NEXT:    FileSize: 16
+#CHECK-NEXT:    MemSize: 16
+#CHECK-NEXT:    Flags [
+#CHECK-NEXT:      PF_R
+#CHECK-NEXT:      PF_X
+#CHECK-NEXT:    ]
+#CHECK-NEXT:    Alignment: 4096
+#CHECK-NEXT:  }
+#CHECK-NEXT:  ProgramHeader {
+#CHECK-NEXT:    Type: PT_LOAD
+#CHECK-NEXT:    Offset: 0x2000
+#CHECK-NEXT:    VirtualAddress: 0x2000
+#CHECK-NEXT:    PhysicalAddress: 0x2000
+#CHECK-NEXT:    FileSize: 16
+#CHECK-NEXT:    MemSize: 16
+#CHECK-NEXT:    Flags [
+#CHECK-NEXT:      PF_R
+#CHECK-NEXT:      PF_W
+#CHECK-NEXT:    ]
+#CHECK-NEXT:    Alignment: 4096
+#CHECK-NEXT:  }
+#CHECK-NEXT:  ProgramHeader {
+#CHECK-NEXT:    Type: PT_GNU_STACK
+#CHECK-NEXT:    Offset: 0x0
+#CHECK-NEXT:    VirtualAddress: 0x0
+#CHECK-NEXT:    PhysicalAddress: 0x0
+#CHECK-NEXT:    FileSize: 0
+#CHECK-NEXT:    MemSize: 0
+#CHECK-NEXT:    Flags [
+#CHECK-NEXT:      PF_R
+#CHECK-NEXT:      PF_W
+#CHECK-NEXT:    ]
+#CHECK-NEXT:    Alignment: 0
+#CHECK-NEXT:  }
+#CHECK-NEXT:]
Index: tools/llvm-objcopy/Object.cpp
===================================================================
--- tools/llvm-objcopy/Object.cpp
+++ tools/llvm-objcopy/Object.cpp
@@ -911,8 +911,20 @@
   // so that we know that anytime ->ParentSegment is set that segment has
   // already had its offset properly set.
   std::vector<Segment *> OrderedSegments;
-  for (auto &Segment : Obj.segments())
-    OrderedSegments.push_back(&Segment);
+  for (auto &Segment : Obj.segments()) {
+    // There could exist so-called marker segments, which are only meant
+    // to signal support of a feature or similar (e.g. GNU_STACK).
+    // These segments do not have any sections, and have 0 FileSize.
+    // Other than that their Offset, VAddr, PAddr, and MemSize are also 0.
+    // Including such a segment in OrderedSegments will produce the lowest
+    // offset of 0, and will let the following segments overwrite the ELF
+    // header.
+    // Here we just check against FileSize as most sensible, since non-zero
+    // MemSize is technically valid, and non-zero Offset should probably
+    // not affect any other segments if FileSize is 0 too.
+    if (Segment.FileSize > 0)
+      OrderedSegments.push_back(&Segment);
+  }
   OrderSegments(OrderedSegments);
   // The size of ELF + program headers will not change so it is ok to assume
   // that the first offset of the first segment is a good place to start