diff --git a/zip/testdata/check_dir/various.txt b/zip/testdata/check_dir/various.txt
index ee843be..4dd757d 100644
--- a/zip/testdata/check_dir/various.txt
+++ b/zip/testdata/check_dir/various.txt
@@ -1,6 +1,7 @@
 -- want --
 valid:
 $work/valid.go
+$work/vendor/modules.txt
 
 omitted:
 $work/.hg_archival.txt: file is inserted by 'hg archive' and is always omitted
@@ -14,6 +15,7 @@ $work/invalid.go': malformed file path "invalid.go'": invalid char '\''
 -- valid.go --
 -- GO.MOD --
 -- invalid.go' --
+-- vendor/modules.txt --
 -- vendor/x/y --
 -- sub/go.mod --
 -- .hg_archival.txt --
diff --git a/zip/testdata/check_dir/various_go123.txt b/zip/testdata/check_dir/various_go123.txt
new file mode 100644
index 0000000..169c059
--- /dev/null
+++ b/zip/testdata/check_dir/various_go123.txt
@@ -0,0 +1,23 @@
+-- want --
+valid:
+$work/go.mod
+$work/valid.go
+$work/vendor/modules.txt
+
+omitted:
+$work/.hg_archival.txt: file is inserted by 'hg archive' and is always omitted
+$work/.git: directory is a version control repository
+$work/sub: directory is in another module
+$work/vendor/x/y: file is in vendor directory
+
+invalid:
+$work/invalid.go': malformed file path "invalid.go'": invalid char '\''
+-- valid.go --
+-- go.mod --
+go 1.23
+-- invalid.go' --
+-- vendor/modules.txt --
+-- vendor/x/y --
+-- sub/go.mod --
+-- .hg_archival.txt --
+-- .git/x --
\ No newline at end of file
diff --git a/zip/testdata/check_dir/various_go124.txt b/zip/testdata/check_dir/various_go124.txt
new file mode 100644
index 0000000..bea7bf4
--- /dev/null
+++ b/zip/testdata/check_dir/various_go124.txt
@@ -0,0 +1,24 @@
+-- want --
+valid:
+$work/go.mod
+$work/valid.go
+
+omitted:
+$work/.hg_archival.txt: file is inserted by 'hg archive' and is always omitted
+$work/.git: directory is a version control repository
+$work/sub: directory is in another module
+$work/vendor/modules.txt: file is in vendor directory
+$work/vendor/x/y: file is in vendor directory
+
+invalid:
+$work/invalid.go': malformed file path "invalid.go'": invalid char '\''
+-- go.mod --
+go 1.24
+-- valid.go --
+-- invalid.go' --
+-- vendor/modules.txt --
+-- vendor/x/y --
+-- sub/go.mod --
+go 1.23
+-- .hg_archival.txt --
+-- .git/x --
diff --git a/zip/testdata/check_files/various.txt b/zip/testdata/check_files/various.txt
index a704a8a..cb312bf 100644
--- a/zip/testdata/check_files/various.txt
+++ b/zip/testdata/check_files/various.txt
@@ -1,6 +1,7 @@
 -- want --
 valid:
 valid.go
+vendor/modules.txt
 
 omitted:
 vendor/x/y: file is in vendor directory
@@ -17,6 +18,7 @@ valid.go: multiple entries for file "valid.go"
 -- GO.MOD --
 -- invalid.go' --
 -- vendor/x/y --
+-- vendor/modules.txt --
 -- sub/go.mod --
 -- .hg_archival.txt --
 -- valid.go --
diff --git a/zip/testdata/check_files/various_go123.txt b/zip/testdata/check_files/various_go123.txt
new file mode 100644
index 0000000..7a34168
--- /dev/null
+++ b/zip/testdata/check_files/various_go123.txt
@@ -0,0 +1,28 @@
+-- want --
+valid:
+valid.go
+go.mod
+vendor/modules.txt
+
+omitted:
+vendor/x/y: file is in vendor directory
+sub/go.mod: file is in another module
+.hg_archival.txt: file is inserted by 'hg archive' and is always omitted
+
+invalid:
+not/../clean: file path is not clean
+invalid.go': malformed file path "invalid.go'": invalid char '\''
+valid.go: multiple entries for file "valid.go"
+-- valid.go --
+-- not/../clean --
+-- go.mod --
+go 1.23
+-- invalid.go' --
+-- vendor/x/y --
+-- vendor/modules.txt --
+-- sub/go.mod --
+-- .hg_archival.txt --
+-- valid.go --
+duplicate
+-- valid.go --
+another duplicate
diff --git a/zip/testdata/check_files/various_go124.txt b/zip/testdata/check_files/various_go124.txt
new file mode 100644
index 0000000..3e8881d
--- /dev/null
+++ b/zip/testdata/check_files/various_go124.txt
@@ -0,0 +1,29 @@
+-- want --
+valid:
+valid.go
+go.mod
+
+omitted:
+vendor/x/y: file is in vendor directory
+vendor/modules.txt: file is in vendor directory
+sub/go.mod: file is in another module
+.hg_archival.txt: file is inserted by 'hg archive' and is always omitted
+
+invalid:
+not/../clean: file path is not clean
+invalid.go': malformed file path "invalid.go'": invalid char '\''
+valid.go: multiple entries for file "valid.go"
+-- valid.go --
+-- not/../clean --
+-- go.mod --
+go 1.24
+-- invalid.go' --
+-- vendor/x/y --
+-- vendor/modules.txt --
+-- sub/go.mod --
+go 1.23
+-- .hg_archival.txt --
+-- valid.go --
+duplicate
+-- valid.go --
+another duplicate
diff --git a/zip/testdata/create/exclude_vendor_go124.txt b/zip/testdata/create/exclude_vendor_go124.txt
new file mode 100644
index 0000000..5559d66
--- /dev/null
+++ b/zip/testdata/create/exclude_vendor_go124.txt
@@ -0,0 +1,15 @@
+path=example.com/m
+version=v1.0.0
+hash=h1:WxQ7ERgHLILawPCiuSwXp5UHul7CUSRRftO8b7GTnV8=
+-- go.mod --
+module example.com/m
+
+go 1.24
+modules.txt is excluded in 1.24+. See golang.org/issue/63395
+-- vendor/modules.txt --
+excluded
+see comment in isVendoredPackage and golang.org/issue/31562.
+-- vendor/example.com/x/x.go --
+excluded
+-- sub/vendor/sub.txt --
+excluded
diff --git a/zip/testdata/create_from_dir/exclude_vendor_go124.txt b/zip/testdata/create_from_dir/exclude_vendor_go124.txt
new file mode 100644
index 0000000..5559d66
--- /dev/null
+++ b/zip/testdata/create_from_dir/exclude_vendor_go124.txt
@@ -0,0 +1,15 @@
+path=example.com/m
+version=v1.0.0
+hash=h1:WxQ7ERgHLILawPCiuSwXp5UHul7CUSRRftO8b7GTnV8=
+-- go.mod --
+module example.com/m
+
+go 1.24
+modules.txt is excluded in 1.24+. See golang.org/issue/63395
+-- vendor/modules.txt --
+excluded
+see comment in isVendoredPackage and golang.org/issue/31562.
+-- vendor/example.com/x/x.go --
+excluded
+-- sub/vendor/sub.txt --
+excluded
diff --git a/zip/vendor_test.go b/zip/vendor_test.go
index 5eb9535..e330401 100644
--- a/zip/vendor_test.go
+++ b/zip/vendor_test.go
@@ -6,17 +6,36 @@ package zip
 
 import "testing"
 
+var pre124 []string = []string{
+	"",
+	"go1.14",
+	"go1.21.0",
+	"go1.22.4",
+	"go1.23",
+	"go1.23.1",
+	"go1.2",
+	"go1.7",
+	"go1.9",
+}
+
 func TestIsVendoredPackage(t *testing.T) {
 	for _, tc := range []struct {
 		path          string
 		want          bool
 		falsePositive bool // is this case affected by https://golang.org/issue/37397?
+		versions      []string
 	}{
-		{path: "vendor/foo/foo.go", want: true},
-		{path: "pkg/vendor/foo/foo.go", want: true},
-		{path: "longpackagename/vendor/foo/foo.go", want: true},
+		{path: "vendor/foo/foo.go", want: true, versions: pre124},
+		{path: "pkg/vendor/foo/foo.go", want: true, versions: pre124},
+		{path: "longpackagename/vendor/foo/foo.go", want: true, versions: pre124},
+		{path: "vendor/vendor.go", want: false, versions: pre124},
+		{path: "vendor/foo/modules.txt", want: true, versions: pre124},
+		{path: "modules.txt", want: false, versions: pre124},
+		{path: "vendor/amodules.txt", want: false, versions: pre124},
 
-		{path: "vendor/vendor.go", want: false},
+		// These test cases were affected by https://golang.org/issue/63395
+		{path: "vendor/modules.txt", want: false, versions: pre124},
+		{path: "vendor/modules.txt", want: true, versions: []string{"go1.24.0", "go1.24", "go1.99.0"}},
 
 		// We ideally want these cases to be false, but they are affected by
 		// https://golang.org/issue/37397, and if we fix them we will invalidate
@@ -24,13 +43,15 @@ func TestIsVendoredPackage(t *testing.T) {
 		{path: "pkg/vendor/vendor.go", falsePositive: true},
 		{path: "longpackagename/vendor/vendor.go", falsePositive: true},
 	} {
-		got := isVendoredPackage(tc.path)
-		want := tc.want
-		if tc.falsePositive {
-			want = true
-		}
-		if got != want {
-			t.Errorf("isVendoredPackage(%q) = %t; want %t", tc.path, got, tc.want)
+		for _, v := range tc.versions {
+			got := isVendoredPackage(tc.path, v)
+			want := tc.want
+			if tc.falsePositive {
+				want = true
+			}
+			if got != want {
+				t.Errorf("isVendoredPackage(%q, %s) = %t; want %t", tc.path, v, got, tc.want)
+			}
 			if tc.falsePositive {
 				t.Logf("(Expected a false-positive due to https://golang.org/issue/37397.)")
 			}
diff --git a/zip/zip.go b/zip/zip.go
index 5aed6e2..9b351c5 100644
--- a/zip/zip.go
+++ b/zip/zip.go
@@ -50,6 +50,7 @@ import (
 	"bytes"
 	"errors"
 	"fmt"
+	"go/version"
 	"io"
 	"os"
 	"os/exec"
@@ -60,6 +61,7 @@ import (
 	"unicode"
 	"unicode/utf8"
 
+	"golang.org/x/mod/modfile"
 	"golang.org/x/mod/module"
 )
 
@@ -193,6 +195,20 @@ func CheckFiles(files []File) (CheckedFiles, error) {
 	return cf, cf.Err()
 }
 
+// parseGoVers extracts the Go version specified in the given go.mod file.
+// It returns an empty string if the version is not found or if an error
+// occurs during file parsing.
+//
+// The version string is in Go toolchain name syntax, prefixed with "go".
+// Examples: "go1.21", "go1.22rc2", "go1.23.0"
+func parseGoVers(file string, data []byte) string {
+	mfile, err := modfile.ParseLax(file, data, nil)
+	if err != nil || mfile.Go == nil {
+		return ""
+	}
+	return "go" + mfile.Go.Version
+}
+
 // checkFiles implements CheckFiles and also returns lists of valid files and
 // their sizes, corresponding to cf.Valid. It omits files in submodules, files
 // in vendored packages, symlinked files, and various other unwanted files.
@@ -217,6 +233,7 @@ func checkFiles(files []File) (cf CheckedFiles, validFiles []File, validSizes []
 	// Files in these directories will be omitted.
 	// These directories will not be included in the output zip.
 	haveGoMod := make(map[string]bool)
+	var vers string
 	for _, f := range files {
 		p := f.Path()
 		dir, base := path.Split(p)
@@ -226,8 +243,21 @@ func checkFiles(files []File) (cf CheckedFiles, validFiles []File, validSizes []
 				addError(p, false, err)
 				continue
 			}
-			if info.Mode().IsRegular() {
-				haveGoMod[dir] = true
+			if !info.Mode().IsRegular() {
+				continue
+			}
+			haveGoMod[dir] = true
+			// Extract the Go language version from the root "go.mod" file.
+			// This ensures we correctly interpret Go version-specific file omissions.
+			// We use f.Open() to handle potential custom Open() implementations
+			// that the underlying File type might have.
+			if base == "go.mod" && dir == "" {
+				if file, err := f.Open(); err == nil {
+					if data, err := io.ReadAll(file); err == nil {
+						vers = version.Lang(parseGoVers("go.mod", data))
+					}
+					file.Close()
+				}
 			}
 		}
 	}
@@ -257,7 +287,7 @@ func checkFiles(files []File) (cf CheckedFiles, validFiles []File, validSizes []
 			addError(p, false, errPathNotRelative)
 			continue
 		}
-		if isVendoredPackage(p) {
+		if isVendoredPackage(p, vers) {
 			// Skip files in vendored packages.
 			addError(p, true, errVendored)
 			continue
@@ -758,7 +788,17 @@ func (fi dataFileInfo) Sys() interface{}   { return nil }
 //
 // Unfortunately, isVendoredPackage reports false positives for files in any
 // non-top-level package whose import path ends in "vendor".
-func isVendoredPackage(name string) bool {
+// The 'vers' parameter specifies the Go version declared in the module's
+// go.mod file and must be a valid Go version according to the
+// go/version.IsValid function.
+// Vendoring behavior has evolved across Go versions, so this function adapts
+// its logic accordingly.
+func isVendoredPackage(name string, vers string) bool {
+	// vendor/modules.txt is a vendored package but was included in 1.23 and earlier.
+	// Remove vendor/modules.txt only for 1.24 and beyond to preserve older checksums.
+	if version.Compare(vers, "go1.24") >= 0 && name == "vendor/modules.txt" {
+		return true
+	}
 	var i int
 	if strings.HasPrefix(name, "vendor/") {
 		i += len("vendor/")
@@ -894,6 +934,12 @@ func (cc collisionChecker) check(p string, isDir bool) error {
 // files, as well as a list of directories and files that were skipped (for
 // example, nested modules and symbolic links).
 func listFilesInDir(dir string) (files []File, omitted []FileError, err error) {
+	// Extract the Go language version from the root "go.mod" file.
+	// This ensures we correctly interpret Go version-specific file omissions.
+	var vers string
+	if data, err := os.ReadFile(filepath.Join(dir, "go.mod")); err == nil {
+		vers = version.Lang(parseGoVers("go.mod", data))
+	}
 	err = filepath.Walk(dir, func(filePath string, info os.FileInfo, err error) error {
 		if err != nil {
 			return err
@@ -908,7 +954,7 @@ func listFilesInDir(dir string) (files []File, omitted []FileError, err error) {
 		// golang.org/issue/31562, described in isVendoredPackage.
 		// We would like Create and CreateFromDir to produce the same result
 		// for a set of files, whether expressed as a directory tree or zip.
-		if isVendoredPackage(slashPath) {
+		if isVendoredPackage(slashPath, vers) {
 			omitted = append(omitted, FileError{Path: slashPath, Err: errVendored})
 			return nil
 		}