diff --git a/private/buf/buffetch/internal/errors.go b/private/buf/buffetch/internal/errors.go
index 9ac81aac50..b1a4c0e564 100644
--- a/private/buf/buffetch/internal/errors.go
+++ b/private/buf/buffetch/internal/errors.go
@@ -48,6 +48,16 @@ func NewCannotSpecifyCommitOrTagWithRefError() error {
 	return errors.New(`cannot specify "commit" or "tag" with "ref"`)
 }
 
+// NewCannotSpecifyMergeBaseWithOtherGitOptionsError is a fetch error.
+func NewCannotSpecifyMergeBaseWithOtherGitOptionsError() error {
+	return errors.New(`"merge_base" cannot be specified with "branch", "commit", "tag", or "ref"`)
+}
+
+// NewMergeBaseOnlyForLocalGitError is a fetch error.
+func NewMergeBaseOnlyForLocalGitError() error {
+	return errors.New(`"merge_base" is only supported for local git references (e.g. ".git#merge_base=main")`)
+}
+
 // NewDepthParseError is a fetch error.
 func NewDepthParseError(s string) error {
 	return fmt.Errorf(`could not parse "depth" value %q`, s)
diff --git a/private/buf/buffetch/internal/git_ref.go b/private/buf/buffetch/internal/git_ref.go
index 9fefd70845..7878173347 100644
--- a/private/buf/buffetch/internal/git_ref.go
+++ b/private/buf/buffetch/internal/git_ref.go
@@ -43,6 +43,7 @@ type gitRef struct {
 	recurseSubmodules bool
 	subDirPath        string
 	filter            string
+	gitMergeBase      string
 }
 
 func newGitRef(
@@ -53,6 +54,7 @@ func newGitRef(
 	recurseSubmodules bool,
 	subDirPath string,
 	filter string,
+	gitMergeBase string,
 ) (*gitRef, error) {
 	gitScheme, path, err := getGitSchemeAndPath(format, path)
 	if err != nil {
@@ -77,6 +79,7 @@ func newGitRef(
 		depth,
 		subDirPath,
 		filter,
+		gitMergeBase,
 	), nil
 }
 
@@ -89,6 +92,7 @@ func newDirectGitRef(
 	depth uint32,
 	subDirPath string,
 	filter string,
+	gitMergeBase string,
 ) *gitRef {
 	return &gitRef{
 		format:            format,
@@ -99,6 +103,7 @@ func newDirectGitRef(
 		recurseSubmodules: recurseSubmodules,
 		subDirPath:        subDirPath,
 		filter:            filter,
+		gitMergeBase:      gitMergeBase,
 	}
 }
 
@@ -134,6 +139,10 @@ func (r *gitRef) Filter() string {
 	return r.filter
 }
 
+func (r *gitRef) GitMergeBase() string {
+	return r.gitMergeBase
+}
+
 func (*gitRef) ref()       {}
 func (*gitRef) bucketRef() {}
 func (*gitRef) gitRef()    {}
diff --git a/private/buf/buffetch/internal/internal.go b/private/buf/buffetch/internal/internal.go
index 9434759da6..1023d819d7 100644
--- a/private/buf/buffetch/internal/internal.go
+++ b/private/buf/buffetch/internal/internal.go
@@ -209,6 +209,10 @@ type GitRef interface {
 	SubDirPath() string
 	// Filter spec to use, see the --filter option in git rev-list.
 	Filter() string
+	// GitMergeBase returns the ref to compute the merge-base with (via "git merge-base HEAD <ref>").
+	// Returns empty string if not set.
+	// Only supported for local git references.
+	GitMergeBase() string
 	gitRef()
 }
 
@@ -221,7 +225,7 @@ func NewGitRef(
 	subDirPath string,
 	filter string,
 ) (GitRef, error) {
-	return newGitRef("", path, gitName, depth, recurseSubmodules, subDirPath, filter)
+	return newGitRef("", path, gitName, depth, recurseSubmodules, subDirPath, filter, "")
 }
 
 // ModuleRef is a module reference.
@@ -357,6 +361,7 @@ func NewDirectParsedGitRef(
 	depth uint32,
 	subDirPath string,
 	filter string,
+	gitMergeBase string,
 ) ParsedGitRef {
 	return newDirectGitRef(
 		format,
@@ -367,6 +372,7 @@ func NewDirectParsedGitRef(
 		depth,
 		subDirPath,
 		filter,
+		gitMergeBase,
 	)
 }
 
@@ -565,6 +571,13 @@ type RawRef struct {
 	// Only set for git formats.
 	// The filter spec to use, see the --filter option in git rev-list.
 	GitFilter string
+	// Only set for git formats.
+	// Specifies a branch or ref to compute the git merge-base with, relative to HEAD.
+	// When set, buf will run "git merge-base HEAD <GitMergeBase>" and use the resulting
+	// commit as the checkout target.
+	// Cannot be specified with GitBranch, GitCommitOrTag, or GitRef.
+	// Only supported for local git references.
+	GitMergeBase string
 	// Only set for archive formats.
 	ArchiveStripComponents uint32
 	// Only set for proto file ref format.
diff --git a/private/buf/buffetch/internal/reader.go b/private/buf/buffetch/internal/reader.go
index fc3ba3b5f1..54c147086c 100644
--- a/private/buf/buffetch/internal/reader.go
+++ b/private/buf/buffetch/internal/reader.go
@@ -363,6 +363,30 @@ func (r *reader) getGitBucket(
 	if err != nil {
 		return nil, nil, err
 	}
+	gitName := gitRef.GitName()
+	if mergeBaseRef := gitRef.GitMergeBase(); mergeBaseRef != "" {
+		if gitRef.GitScheme() != GitSchemeLocal {
+			return nil, nil, NewMergeBaseOnlyForLocalGitError()
+		}
+		// gitRef.Path() is the normalized path to the git repository (e.g. ".git").
+		// We need the directory containing it to run "git merge-base".
+		localPath := normalpath.Unnormalize(gitRef.Path())
+		absPath, err := filepath.Abs(localPath)
+		if err != nil {
+			return nil, nil, fmt.Errorf("could not resolve local git path: %w", err)
+		}
+		// Use the parent directory if the path is a .git directory,
+		// otherwise use the path directly (worktree or bare repo).
+		gitDir := absPath
+		if filepath.Base(absPath) == ".git" {
+			gitDir = filepath.Dir(absPath)
+		}
+		mergeBaseCommit, err := git.GetMergeBase(ctx, container, gitDir, mergeBaseRef)
+		if err != nil {
+			return nil, nil, err
+		}
+		gitName = git.NewRefName(mergeBaseCommit)
+	}
 	readWriteBucket := storagemem.NewReadWriteBucket()
 	if err := r.gitCloner.CloneToBucket(
 		ctx,
@@ -371,7 +395,7 @@ func (r *reader) getGitBucket(
 		gitRef.Depth(),
 		readWriteBucket,
 		git.CloneToBucketOptions{
-			Name:              gitRef.GitName(),
+			Name:              gitName,
 			RecurseSubmodules: gitRef.RecurseSubmodules(),
 			SubDir:            gitRef.SubDirPath(),
 			Filter:            gitRef.Filter(),
diff --git a/private/buf/buffetch/internal/ref_parser.go b/private/buf/buffetch/internal/ref_parser.go
index a2c20ebe8e..f77acdbce2 100644
--- a/private/buf/buffetch/internal/ref_parser.go
+++ b/private/buf/buffetch/internal/ref_parser.go
@@ -142,6 +142,8 @@ func (a *refParser) getRawRef(
 			rawRef.GitCommitOrTag = value
 		case "ref":
 			rawRef.GitRef = value
+		case "merge_base":
+			rawRef.GitMergeBase = value
 		case "filter":
 			rawRef.GitFilter = value
 		case "depth":
@@ -191,8 +193,8 @@ func (a *refParser) getRawRef(
 	if rawRef.Format == "git" && rawRef.GitDepth == 0 {
 		// Default to 1
 		rawRef.GitDepth = 1
-		if rawRef.GitRef != "" {
-			// Default to 50 when using ref
+		if rawRef.GitRef != "" || rawRef.GitMergeBase != "" {
+			// Default to 50 when using ref or merge_base
 			rawRef.GitDepth = 50
 		}
 	}
@@ -347,8 +349,11 @@ func (a *refParser) validateRawRef(
 		if rawRef.GitRef != "" && rawRef.GitCommitOrTag != "" {
 			return NewCannotSpecifyCommitOrTagWithRefError()
 		}
+		if rawRef.GitMergeBase != "" && (rawRef.GitBranch != "" || rawRef.GitCommitOrTag != "" || rawRef.GitRef != "") {
+			return NewCannotSpecifyMergeBaseWithOtherGitOptionsError()
+		}
 	} else {
-		if rawRef.GitBranch != "" || rawRef.GitCommitOrTag != "" || rawRef.GitRef != "" || rawRef.GitRecurseSubmodules || rawRef.GitDepth > 0 {
+		if rawRef.GitBranch != "" || rawRef.GitCommitOrTag != "" || rawRef.GitRef != "" || rawRef.GitMergeBase != "" || rawRef.GitRecurseSubmodules || rawRef.GitDepth > 0 {
 			return NewOptionsInvalidForFormatError(rawRef.Format, displayName, "git options set")
 		}
 	}
@@ -522,6 +527,7 @@ func getGitRef(
 		rawRef.GitRecurseSubmodules,
 		rawRef.SubDirPath,
 		rawRef.GitFilter,
+		rawRef.GitMergeBase,
 	)
 }
 
diff --git a/private/buf/buffetch/internal/ref_parser_test.go b/private/buf/buffetch/internal/ref_parser_test.go
index c28612e17b..a97061f7b1 100644
--- a/private/buf/buffetch/internal/ref_parser_test.go
+++ b/private/buf/buffetch/internal/ref_parser_test.go
@@ -15,9 +15,12 @@
 package internal
 
 import (
+	"context"
 	"testing"
 
+	"github.com/bufbuild/buf/private/pkg/slogtestext"
 	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
 )
 
 func TestGetRawPathAndOptionsError(t *testing.T) {
@@ -85,3 +88,38 @@ func testGetRawPathAndOptionsError(
 		assert.EqualError(t, err, expectedErr.Error())
 	})
 }
+
+func TestRefParserGitMergeBaseValidation(t *testing.T) {
+	t.Parallel()
+	parser := newRefParser(slogtestext.NewLogger(t), WithGitFormat("git"))
+	ctx := context.Background()
+
+	t.Run("valid_merge_base", func(t *testing.T) {
+		t.Parallel()
+		parsedRef, err := parser.getParsedRef(ctx, "path/to/repo#format=git,merge_base=main", nil)
+		require.NoError(t, err)
+		gitRef, ok := parsedRef.(GitRef)
+		require.True(t, ok, "expected GitRef")
+		assert.Equal(t, "main", gitRef.GitMergeBase())
+		assert.Equal(t, uint32(50), gitRef.Depth())
+		assert.Nil(t, gitRef.GitName())
+	})
+
+	t.Run("merge_base_with_branch", func(t *testing.T) {
+		t.Parallel()
+		_, err := parser.getParsedRef(ctx, "path/to/repo#format=git,merge_base=main,branch=feature", nil)
+		assert.EqualError(t, err, NewCannotSpecifyMergeBaseWithOtherGitOptionsError().Error())
+	})
+
+	t.Run("merge_base_with_ref", func(t *testing.T) {
+		t.Parallel()
+		_, err := parser.getParsedRef(ctx, "path/to/repo#format=git,merge_base=main,ref=abc123", nil)
+		assert.EqualError(t, err, NewCannotSpecifyMergeBaseWithOtherGitOptionsError().Error())
+	})
+
+	t.Run("merge_base_with_commit", func(t *testing.T) {
+		t.Parallel()
+		_, err := parser.getParsedRef(ctx, "path/to/repo#format=git,merge_base=main,commit=abc123", nil)
+		assert.EqualError(t, err, NewCannotSpecifyMergeBaseWithOtherGitOptionsError().Error())
+	})
+}
diff --git a/private/buf/buffetch/ref_parser_test.go b/private/buf/buffetch/ref_parser_test.go
index 8b6d73517f..896735d021 100644
--- a/private/buf/buffetch/ref_parser_test.go
+++ b/private/buf/buffetch/ref_parser_test.go
@@ -257,6 +257,7 @@ func TestGetParsedRefSuccess(t *testing.T) {
 			1,
 			"",
 			"",
+			"",
 		),
 		"path/to/dir.git",
 	)
@@ -271,6 +272,7 @@ func TestGetParsedRefSuccess(t *testing.T) {
 			40,
 			"",
 			"",
+			"",
 		),
 		"path/to/dir.git#depth=40",
 	)
@@ -285,6 +287,7 @@ func TestGetParsedRefSuccess(t *testing.T) {
 			1,
 			"",
 			"",
+			"",
 		),
 		"path/to/dir.git#branch=main",
 	)
@@ -299,6 +302,7 @@ func TestGetParsedRefSuccess(t *testing.T) {
 			1,
 			"",
 			"",
+			"",
 		),
 		"file:///path/to/dir.git#branch=main",
 	)
@@ -313,6 +317,7 @@ func TestGetParsedRefSuccess(t *testing.T) {
 			1,
 			"",
 			"",
+			"",
 		),
 		"path/to/dir.git#tag=v1.0.0",
 	)
@@ -327,6 +332,7 @@ func TestGetParsedRefSuccess(t *testing.T) {
 			1,
 			"",
 			"",
+			"",
 		),
 		"http://hello.com/path/to/dir.git#branch=main",
 	)
@@ -341,6 +347,7 @@ func TestGetParsedRefSuccess(t *testing.T) {
 			1,
 			"",
 			"",
+			"",
 		),
 		"https://hello.com/path/to/dir.git#branch=main",
 	)
@@ -355,6 +362,7 @@ func TestGetParsedRefSuccess(t *testing.T) {
 			1,
 			"",
 			"",
+			"",
 		),
 		"ssh://user@hello.com:path/to/dir.git#branch=main",
 	)
@@ -369,6 +377,7 @@ func TestGetParsedRefSuccess(t *testing.T) {
 			50,
 			"",
 			"",
+			"",
 		),
 		"ssh://user@hello.com:path/to/dir.git#ref=refs/remotes/origin/HEAD",
 	)
@@ -383,6 +392,7 @@ func TestGetParsedRefSuccess(t *testing.T) {
 			50,
 			"",
 			"",
+			"",
 		),
 		"ssh://user@hello.com:path/to/dir.git#ref=refs/remotes/origin/HEAD,branch=main",
 	)
@@ -397,6 +407,7 @@ func TestGetParsedRefSuccess(t *testing.T) {
 			10,
 			"",
 			"",
+			"",
 		),
 		"ssh://user@hello.com:path/to/dir.git#ref=refs/remotes/origin/HEAD,depth=10",
 	)
@@ -411,6 +422,7 @@ func TestGetParsedRefSuccess(t *testing.T) {
 			10,
 			"",
 			"",
+			"",
 		),
 		"ssh://user@hello.com:path/to/dir.git#ref=refs/remotes/origin/HEAD,branch=main,depth=10",
 	)
@@ -425,6 +437,7 @@ func TestGetParsedRefSuccess(t *testing.T) {
 			1,
 			"foo/bar",
 			"",
+			"",
 		),
 		"path/to/dir.git#subdir=foo/bar",
 	)
@@ -439,6 +452,7 @@ func TestGetParsedRefSuccess(t *testing.T) {
 			1,
 			"",
 			"",
+			"",
 		),
 		"path/to/dir.git#subdir=.",
 	)
@@ -453,6 +467,7 @@ func TestGetParsedRefSuccess(t *testing.T) {
 			1,
 			"",
 			"",
+			"",
 		),
 		"path/to/dir.git#subdir=foo/..",
 	)
@@ -467,6 +482,7 @@ func TestGetParsedRefSuccess(t *testing.T) {
 			1,
 			"",
 			"",
+			"",
 		),
 		"git://user@hello.com:path/to/dir.git#branch=main",
 	)
@@ -481,6 +497,7 @@ func TestGetParsedRefSuccess(t *testing.T) {
 			1,
 			"",
 			"",
+			"",
 		),
 		"git://path/to/dir.git#branch=main",
 	)
@@ -495,6 +512,7 @@ func TestGetParsedRefSuccess(t *testing.T) {
 			1,
 			"subdir",
 			"tree:0",
+			"",
 		),
 		"git://path/to/dir.git#branch=main,filter=tree:0,subdir=subdir",
 	)
@@ -842,6 +860,7 @@ func TestGetParsedRefSuccess(t *testing.T) {
 			1,
 			"",
 			"",
+			"",
 		),
 		"/path/to/dir#branch=main,format=git",
 	)
@@ -856,6 +875,7 @@ func TestGetParsedRefSuccess(t *testing.T) {
 			1,
 			"",
 			"",
+			"",
 		),
 		"/path/to/dir#format=git,branch=main/foo",
 	)
@@ -870,6 +890,7 @@ func TestGetParsedRefSuccess(t *testing.T) {
 			1,
 			"",
 			"",
+			"",
 		),
 		"path/to/dir#tag=main/foo,format=git",
 	)
@@ -884,6 +905,7 @@ func TestGetParsedRefSuccess(t *testing.T) {
 			1,
 			"",
 			"",
+			"",
 		),
 		"path/to/dir#format=git,tag=main/foo",
 	)
@@ -898,6 +920,7 @@ func TestGetParsedRefSuccess(t *testing.T) {
 			1,
 			"",
 			"",
+			"",
 		),
 		"path/to/dir#format=git,tag=main/foo,recurse_submodules=true",
 	)
@@ -912,6 +935,7 @@ func TestGetParsedRefSuccess(t *testing.T) {
 			1,
 			"",
 			"",
+			"",
 		),
 		"path/to/dir#format=git,tag=main/foo,recurse_submodules=false",
 	)
@@ -926,6 +950,7 @@ func TestGetParsedRefSuccess(t *testing.T) {
 			50,
 			"",
 			"",
+			"",
 		),
 		"path/to/dir#format=git,ref=refs/remotes/origin/HEAD",
 	)
@@ -940,6 +965,7 @@ func TestGetParsedRefSuccess(t *testing.T) {
 			10,
 			"",
 			"",
+			"",
 		),
 		"path/to/dir#format=git,ref=refs/remotes/origin/HEAD,depth=10",
 	)
diff --git a/private/pkg/git/git.go b/private/pkg/git/git.go
index ed47fa01ce..724942b477 100644
--- a/private/pkg/git/git.go
+++ b/private/pkg/git/git.go
@@ -312,6 +312,31 @@ func GetCurrentHEADGitCommit(
 	return strings.TrimSpace(stdout.String()), nil
 }
 
+// GetMergeBase returns the best common ancestor commit between HEAD and the
+// given ref in the git repository that contains dir, equivalent to running
+// "git merge-base HEAD <ref>". Returns the full commit hash with no trailing whitespace.
+func GetMergeBase(
+	ctx context.Context,
+	envContainer app.EnvContainer,
+	dir string,
+	ref string,
+) (string, error) {
+	stdout := bytes.NewBuffer(nil)
+	stderr := bytes.NewBuffer(nil)
+	if err := xexec.Run(
+		ctx,
+		gitCommand,
+		xexec.WithArgs("merge-base", "HEAD", ref),
+		xexec.WithStdout(stdout),
+		xexec.WithStderr(stderr),
+		xexec.WithDir(dir),
+		xexec.WithEnv(app.Environ(envContainer)),
+	); err != nil {
+		return "", fmt.Errorf("failed to compute merge-base between HEAD and %s: %w: %s", ref, err, stderr.String())
+	}
+	return strings.TrimSpace(stdout.String()), nil
+}
+
 // GetRefsForGitCommitAndRemote returns all refs pointing to a given commit based on the
 // given remote for the given directory. Querying the remote for refs information requires
 // passing the environment for permissions.