A thrombectomy catheter system with occluder and method of using same for removal of tissue, such as thrombus and the like, from a vessel in the body. Multiple catheters and an occluder-bearing guidewire tube at a thrombus site provide for expandable deployment of a compliant occluder against the vasculature walls distal to the thrombus. The expanded occluder is maneuvered proximally to urge thrombus into close proximity with a retractable capture cone located distally on a capture catheter where the thrombus is dislodged, entrained, and broken into pieces by the action of a fluid jet emanator and then evacuated through the capture catheter.
