First off, as Belial pointed out, the Living Dead can't die except via a means exploiting a specific weakness. So the worst case scenario for the BCV is that he's taken out and -- assuming measures aren't taken to prevent it -- recovers eventually.
That said, I agree with others that the train should be treated as more or less a weapon for purposes of the mechanics. So maybe the character uses Athletics to attack with the weapon:5 train (to time the throw properly). If the BCV is 'taken out', then he is 'dead' ... until he gets better. If not, then pick your resolution: perhaps he leaps back up to the platform jst before the train arrives, suffering no more than a glancing blow (or not so glancing, depending on the attack's results). Or he leaps up at the last moment and clings to the ceiling of the tunnel, taking the glancing blow, then leaps down after the train passes. Or similarly, he ducks down between the tracks, using his strength to avoid getting sucked into the train's undercarriage. Or he smashes through the front windshield of the train, surprising the driver (and draining him dry to heal some damage via Blood Drinker). Or he 'sticks' to the front of the train, letting it carry him to safety. Etc.
I think I was running the scene, I'd probably opt to play the scene out as a concession. The vampire gets to narrate the result, which would be the "breaking through the cab and eating the driver" option because it appeals to me. The players make no attack roll (beyond the maneuver they used to get the vamp there in the first place) because it's a concession, but I'd mix in some environmental damage reduced by an appropriate roll (in this case, probably the Athletics limited by Might or vice versa dodge the train through its window). This resulting damage might well be mitigated entirely by Toughness combined by a refreshing snack. In the aftermath, of course, the runaway train might be brought to a stop in time by the passengers ... or it might result in a spectacular crash with the size effect of concealing the fate of the BCV. Well, until a later scene in which it returns for vengeance, of course.
But your mileage might vary.