diff --git a/src/cmd/go/internal/modload/init.go b/src/cmd/go/internal/modload/init.go
index cdcfbeb8ded..23f4efd02ad 100644
--- a/src/cmd/go/internal/modload/init.go
+++ b/src/cmd/go/internal/modload/init.go
@@ -610,6 +610,9 @@ func UpdateWorkFile(wf *modfile.WorkFile) {
 	missingModulePaths := map[string]string{} // module directory listed in file -> abspath modroot
 
 	for _, d := range wf.Use {
+		if d.Path == "" {
+			continue // d is marked for deletion.
+		}
 		modRoot := d.Path
 		if d.ModulePath == "" {
 			missingModulePaths[d.Path] = modRoot
diff --git a/src/cmd/go/testdata/script/work_use_issue50958.txt b/src/cmd/go/testdata/script/work_use_issue50958.txt
new file mode 100644
index 00000000000..7a25531f3d1
--- /dev/null
+++ b/src/cmd/go/testdata/script/work_use_issue50958.txt
@@ -0,0 +1,17 @@
+go work use -r .
+cmp go.work go.work.want
+
+-- go.mod --
+module example
+go 1.18
+-- go.work --
+go 1.18
+
+use sub
+-- go.work.want --
+go 1.18
+
+use .
+-- sub/README.txt --
+This directory no longer contains a go.mod file.
+