A pneumatically-operated thrombectomy catheter deployment system having a plurality of components collectively acting as a drive unit, including a double-acting air cylinder, a reciprocating assembly including a positionable four-way valve, a high pressure pump, an effluent pump, a compressed air tank, and other closely related components. The double-acting air cylinder is reciprocatingly driven by the complement of the drive unit components to provide high pressure saline for use in the thrombectomy catheter and to exhaust effluent from the system. A plurality of preconnected components are connected to the drive unit including a thrombectomy catheter, a saline supply bag, an effluent collection bag, connection tubes, and other closely related components.