Disclosed herein are an apparatus and method for manufacturing a balloon catheter in which a non-contact type laser perforator and printer are separately provided above a primary extruder such that inflation apertures can be uniformly perforated through a non-vulcanized lumen tube and simultaneously, tube cutting positions can be printed on the lumen tube at positions uniformly spaced apart from the inflation apertures without stopping a primary extrusion process. Also, a bond preventing agent layer is coated on the lumen tube at balloon inflating portions prior to cutting the tube, to facilitate a secondary extrusion of the tube. With this configuration, continuous and accurate perforation of inflation apertures is possible and automatic tube cutting can be achieved based on the printed tube cutting positions. Also, the present invention can compensate for a time delay due to a bond preventing agent application process and achieve high productivity and minimized loss of material.