An aftertreatment module for use with an engine is disclosed. The aftertreatment module may have a plurality of inlets configured to direct exhaust in a first flow direction into the aftertreatment module. The aftertreatment module may also have a mixing duct configured to receive exhaust from the plurality of inlets, and a branching passage in fluid communication with the mixing duct. The branching passage may be configured to redirect exhaust from the mixing duct into separate flows that exit the aftertreatment module in a second flow direction opposite the first flow direction.