An aftertreatment module for use with an engine is disclosed. The aftertreatment module may have a first chamber with an inlet, and at least one catalyst substrate disposed in the first chamber in a flow path through the inlet and having a flow direction from an inlet face to an outlet face in general alignment with the flow path. The aftertreatment module may also have a second chamber with at least one outlet in general alignment with the flow direction through the inlet. The aftertreatment module may further have at least one noise attenuation passage fluidly connecting the first chamber with the second chamber. The at least one noise attenuation passage may be oriented generally orthogonal to the inlet and the at least one outlet and be located between the inlet and the outlet face of the at least one catalyst substrate.