Cherepovets sits on the main railway line between Moscow and Arkhangelsk, via Vologda. Trains from Moscow's Yaroslavsky station take roughly four hours to Vologda and another hour or so to Cherepovets, depending on the service. Several daily trains make the full run, and overnight services run through to Arkhangelsk. The station is on the northern edge of the city centre.
Vologda is an easy hour away by rail and makes a good base for the region — it has more to see, better accommodation options, and a well-preserved historic centre. From Vologda, Cherepovets is manageable as a day trip, or you can continue north toward Arkhangelsk or east toward the Urals.