Troupe generally applies to groups that travel from one venue to another, and may sometimes be used for groups that tour for only one show. Repertory company refers specifically to a group that performs multiple successive shows together, and usually has a stationary home theatre (though repertory companies may also tour). From Oxford Dictionaries:
treated as singular or plural The actors taking part in a play, film, or other production.
A group of dancers, actors, or other entertainers who tour to different venues.
repertory company NOUN
A theatrical company that performs plays from its repertoire for regular, short periods of time, moving on from one play to another.