An aftertreatment module is disclosed for use with an engine. The aftertreatment module may have an inlet housing at least partially defining an inlet passage for exhaust, and at least one mixer disposed in the inlet passage. The aftertreatment module may also have an outlet housing at least partially defining an outlet passage for exhaust, and a catalyst housing removably connected between the inlet housing and the outlet housing. The aftertreatment module may further have a plurality of catalyst substrates configured to be mounted in the catalyst housing, to receive exhaust from the inlet passage in parallel, and to discharge exhaust to the outlet housing in parallel.