If the flux capacitor wasn't enough evidence that the train doesn't run on any standard time system, the Conductor's pocket watch is a further indication.
Throughout the journey to the North Pole, he's very focused on getting there on time, and he's often shown checking his watch in a frantic manner.
Toward the end of the movie, the inside of his pocket watch is finally visible. But instead of having a regular clock face, the hands point to sections labeled "On Time," "Early," "Still," and "Late" with various subcategories.