diff --git a/go/tools/builders/BUILD.bazel b/go/tools/builders/BUILD.bazel
index cf8488b759..97f533aaf0 100644
--- a/go/tools/builders/BUILD.bazel
+++ b/go/tools/builders/BUILD.bazel
@@ -121,6 +121,7 @@ go_tool_binary(
 go_tool_binary(
     name = "go-protoc",
     srcs = [
+        "env.go",
         "flags.go",
         "protoc.go",
     ],
diff --git a/go/tools/builders/compile.go b/go/tools/builders/compile.go
index ff20c9ff3f..08f138501d 100644
--- a/go/tools/builders/compile.go
+++ b/go/tools/builders/compile.go
@@ -49,6 +49,7 @@ func run(args []string) error {
 	if err := goenv.update(); err != nil {
 		return err
 	}
+	absOutput := abs(*output) // required to work with long paths on Windows
 
 	var matcher func(f *goMetadata) bool
 	switch *testfilter {
@@ -80,7 +81,7 @@ func run(args []string) error {
 		}
 	}
 	if len(files) <= 0 {
-		return ioutil.WriteFile(*output, []byte(""), 0644)
+		return ioutil.WriteFile(absOutput, []byte(""), 0644)
 	}
 
 	goargs := []string{"tool", "compile"}
@@ -102,7 +103,7 @@ func run(args []string) error {
 		goargs = append(goargs, "-importmap", mapping)
 		strictdeps = append(strictdeps, source)
 	}
-	goargs = append(goargs, "-pack", "-o", *output)
+	goargs = append(goargs, "-pack", "-o", absOutput)
 	goargs = append(goargs, flags.Args()...)
 	for _, f := range files {
 		goargs = append(goargs, f.filename)
diff --git a/go/tools/builders/env.go b/go/tools/builders/env.go
index cbc23c5eea..ca272b73c9 100644
--- a/go/tools/builders/env.go
+++ b/go/tools/builders/env.go
@@ -41,6 +41,10 @@ type GoEnv struct {
 	ld_flags     multiFlag
 }
 
+// abs returns the absolute representation of path. Some tools/APIs require
+// absolute paths to work correctly. Most notably, golang on Windows cannot
+// handle relative paths to files whose absolute path is > ~250 chars, while
+// it can handle absolute paths. See http://goo.gl/eqeWjm.
 func abs(path string) string {
 	if abs, err := filepath.Abs(path); err != nil {
 		return path
diff --git a/go/tools/builders/filter.go b/go/tools/builders/filter.go
index d000987ffd..e80aa011c9 100644
--- a/go/tools/builders/filter.go
+++ b/go/tools/builders/filter.go
@@ -37,7 +37,7 @@ type goMetadata struct {
 func readFiles(bctx build.Context, inputs []string) ([]*goMetadata, error) {
 	outputs := []*goMetadata{}
 	for _, input := range inputs {
-		if m, err := readGoMetadata(bctx, input, true); err != nil {
+		if m, err := readGoMetadata(bctx, abs(input), true); err != nil {
 			return nil, err
 		} else if m.matched {
 			outputs = append(outputs, m)
diff --git a/go/tools/builders/filter_test.go b/go/tools/builders/filter_test.go
index ec887c440a..e7ca86507c 100644
--- a/go/tools/builders/filter_test.go
+++ b/go/tools/builders/filter_test.go
@@ -124,3 +124,8 @@ func runTest(t *testing.T, bctx build.Context, inputs []string, expect []string)
 		t.Errorf("filter %v,%v,%v,%v: expect %v got %v", bctx.GOOS, bctx.GOARCH, bctx.CgoEnabled, bctx.BuildTags, expect, got)
 	}
 }
+
+// abs is a dummy env.go abs to avoid depending on env.go and flags.go.
+func abs(p string) string {
+	return p
+}
diff --git a/go/tools/builders/protoc.go b/go/tools/builders/protoc.go
index 15ddd795f8..c0e52afd46 100644
--- a/go/tools/builders/protoc.go
+++ b/go/tools/builders/protoc.go
@@ -57,6 +57,17 @@ func run(args []string) error {
 	if err := flags.Parse(args); err != nil {
 		return err
 	}
+
+	// Output to a temporary folder and then move the contents into place below.
+	// This is to work around long file paths on Windows.
+	tmpDir, err := ioutil.TempDir("", "go_proto")
+	if err != nil {
+		return err
+	}
+	tmpDir = abs(tmpDir)        // required to work with long paths on Windows
+	absOutPath := abs(*outPath) // required to work with long paths on Windows
+	defer os.RemoveAll(tmpDir)
+
 	pluginBase := filepath.Base(*plugin)
 	pluginName := strings.TrimSuffix(
 		strings.TrimPrefix(filepath.Base(*plugin), "protoc-gen-"), ".exe")
@@ -64,7 +75,7 @@ func run(args []string) error {
 		options = append(options, fmt.Sprintf("M%v", m))
 	}
 	protoc_args := []string{
-		fmt.Sprintf("--%v_out=%v:%v", pluginName, strings.Join(options, ","), *outPath),
+		fmt.Sprintf("--%v_out=%v:%v", pluginName, strings.Join(options, ","), tmpDir),
 		"--plugin", fmt.Sprintf("%v=%v", strings.TrimSuffix(pluginBase, ".exe"), *plugin),
 		"--descriptor_set_in", strings.Join(descriptors, string(os.PathListSeparator)),
 	}
@@ -95,28 +106,45 @@ func run(args []string) error {
 		}
 	}
 	// Walk the generated files
-	filepath.Walk(*outPath, func(path string, f os.FileInfo, err error) error {
-		if !strings.HasSuffix(path, ".go") {
+	filepath.Walk(tmpDir, func(path string, f os.FileInfo, err error) error {
+		relPath, err := filepath.Rel(tmpDir, path)
+		if err != nil {
+			return err
+		}
+		if relPath == "." {
 			return nil
 		}
-		info := files[path]
-		if info != nil {
-			info.created = true
+
+		if f.IsDir() {
+			if err := os.Mkdir(filepath.Join(absOutPath, relPath), f.Mode()); !os.IsExist(err) {
+				return err
+			}
 			return nil
 		}
-		info = &genFileInfo{
+
+		if !strings.HasSuffix(path, ".go") {
+			return nil
+		}
+
+		info := &genFileInfo{
 			path:    path,
 			base:    filepath.Base(path),
 			created: true,
 		}
-		files[path] = info
+
+		if foundInfo, ok := files[relPath]; ok {
+			foundInfo.created = true
+			foundInfo.from = info
+			return nil
+		}
+		files[relPath] = info
 		copyTo := byBase[info.base]
 		switch {
 		case copyTo == nil:
 			// Unwanted output
 		case !copyTo.unique:
 			// not unique, no copy allowed
-		case info.from != nil:
+		case copyTo.from != nil:
 			copyTo.ambiguious = true
 			info.ambiguious = true
 		default:
@@ -138,7 +166,7 @@ func run(args []string) error {
 			if err != nil {
 				return err
 			}
-			if err := ioutil.WriteFile(f.path, data, 0644); err != nil {
+			if err := ioutil.WriteFile(abs(f.path), data, 0644); err != nil {
 				return err
 			}
 		case !f.expected:
@@ -149,6 +177,7 @@ func run(args []string) error {
 			return errors.New(buf.String())
 		}
 	}
+
 	return nil
 }