The vote was unanimous, and the rules go into effect immediately.
The new rules come after a deadly accident earlier this month during the BART strike in which two BART workers were killed while inspecting tracks near Walnut Creek. A trainee was operating the train at the time.
Under the new rules, transit agencies must immediately create a three-way communications system between central command, train operators and wayside workers.
The rules also cover San Francisco's Muni and the Santa Clara Valley Transportation Authority.