"Va-t-il" alone does mean "is he going," but you have to look at the whole phrase.
"Où va-t-il" where is he going? "Comment va-t-il" how is he doing?
This is idiomatic in French. You can't always translate word-for-word from French to English, because the two languages have different ways of saying things.
When you have an inversion of a verb ending in a vowel and the pronouns il, elle, or on, you must add a "t" between the two words for pronunciation purposes. This is called a euphonic inversion and it is required in written form as well as spoken.