Index: include-fixer/IncludeFixer.cpp
===================================================================
--- include-fixer/IncludeFixer.cpp
+++ include-fixer/IncludeFixer.cpp
@@ -25,6 +25,31 @@
 namespace include_fixer {
 namespace {
 
+// Returns a relative filepath to FilePath from Dir.
+// For example:
+//   RelativePath("/foo/bar", "/foo") => "bar"
+//   RelativePath("/foo/bar/test", "foo/bar/include") => "../test"
+std::string RelativePath(StringRef FilePath, StringRef Dir) {
+  SmallString<256> Result;
+  SmallVector<StringRef, 5> FilePathComponents;
+  SmallVector<StringRef, 5> DirComponents;
+  FilePath.split(FilePathComponents, '/');
+  Dir.split(DirComponents, '/');
+
+  for (size_t i = 0, j = 0;
+      i < FilePathComponents.size() && j < DirComponents.size();
+      ++i, ++j) {
+    if (FilePathComponents[i] != DirComponents[j]) {
+       for (size_t x = 0; x < DirComponents.size() - j; ++x)
+         llvm::sys::path::append(Result, "..");
+       for (;i < FilePathComponents.size(); ++i)
+         llvm::sys::path::append(Result, FilePathComponents[i]);
+       break;
+    }
+  }
+  return Result.str();
+}
+
 class Action;
 
 class PreprocessorHooks : public clang::PPCallbacks {
@@ -171,8 +196,16 @@
 
     // Get the FileEntry for the include.
     StringRef StrippedInclude = Include.trim("\"<>");
+
+    auto BuildDir = SourceManager.getFileManager()
+                          .getVirtualFileSystem()
+                          ->getCurrentWorkingDirectory();
+    if (!BuildDir)
+      return Include;
+    StringRef PathRelativeToBuildDir = RelativePath(StrippedInclude, *BuildDir);
+
     const FileEntry *Entry =
-        SourceManager.getFileManager().getFile(StrippedInclude);
+        SourceManager.getFileManager().getFile(PathRelativeToBuildDir);
 
     // If the file doesn't exist return the path from the database.
     // FIXME: This should never happen.
Index: test/include-fixer/Inputs/database_template.json
===================================================================
--- /dev/null
+++ test/include-fixer/Inputs/database_template.json
@@ -0,0 +1,7 @@
+[
+{
+  "directory": "test_dir/build",
+  "command": "clang++ -I../include -o foo.o test_dir/src/foo.cpp",
+  "file": "test_dir/src/foo.cpp"
+}
+]
Index: test/include-fixer/Inputs/yaml_db_template.yaml
===================================================================
--- /dev/null
+++ test/include-fixer/Inputs/yaml_db_template.yaml
@@ -0,0 +1,11 @@
+---
+Name:           foo
+Contexts:
+  - ContextType:     Namespace
+    ContextName:     a
+  - ContextType:     Namespace
+    ContextName:     b
+FilePath:        test_dir/foo.h
+LineNumber:      1
+Type:            Class
+...
Index: test/include-fixer/include-path.cpp
===================================================================
--- /dev/null
+++ test/include-fixer/include-path.cpp
@@ -0,0 +1,14 @@
+// REQUIRES: shell
+// RUN: mkdir -p %T/include-fixer/include
+// RUN: mkdir -p %T/include-fixer/build
+// RUN: mkdir -p %T/include-fixer/src
+// RUN: sed 's|test_dir|%T/include-fixer|g' %S/Inputs/database_template.json > %T/include-fixer/build/compile_commands.json
+// RUN: sed 's|test_dir|%T/include-fixer/include|g' %S/Inputs/yaml_db_template.yaml > %T/include-fixer/build/fake_yaml_db.yaml
+// RUN: echo 'b::a::foo f;' > %T/include-fixer/src/foo.cpp
+// RUN: touch %T/include/fixer/include/foo.h
+// RUN: cd %T/include-fixer/build
+// RUN: clang-include-fixer -db=yaml -input=fake_yaml_db.yaml -p=. %T/include-fixer/src/foo.cpp
+// RUN: FileCheck -input-file=%T/include-fixer/src/foo.cpp %s
+
+// CHECK: #include "foo.h"
+// CHECK: b::a::foo f;