The invention is directed towards a system and method for decontaminating a device. The system comprises a chamber defining an enclosed space and includes a pump. The enclosed space is configured to withstand pressure changes within the space and receive a device that includes a lumen. The system includes a controller configured to control a temperature and pressure within the chamber, a vacuum pump in fluid communication with the enclosed space, and a source of a decontaminating substance. A vaporizer or atomizer is in fluid communication with the source of the decontaminating substance and is configured to provide a vaporized decontaminating substance within the enclosed space. The pump has an inlet and an outlet. One of the inlet and outlet is in fluid communication with the enclosed space of the chamber and the other of the inlet and outlet is configured to be in fluid communication with the lumen.