A condensate management system for an air conditioning condensate drainage system is provided. The condensate management system may comprise an inlet and an outlet; a primary condensate flow path from the inlet to the outlet; a check valve disposed along the primary condensate flow path; a flush path from the inlet to the outlet; a pump coupled to the flush path; and a logic panel configured to actuate the pump to a flushing mode. The check valve may be configured to allow fluid flow from the inlet to the outlet. When the logic panel is configured to actuate the pump to the flushing mode, the pump is configured to exert a negative pressure at the inlet and a positive pressure at the outlet. Other system and methods to flush a condensate drain system are also described.