We developed a new patterning method for bacteriorhodopsin (bR) thin films using UV light irradiation. The proton pump function of bR thin films can be deactivated with UV light irradiation. Inactivation of the proton pump function of bR is related to structural changes or photo-bleaching of the retinal in bR using UV light exposure, which was confirmed with absorption and Raman spectroscopy measurements. Utilizing inactivation of the proton pump function with UV light irradiation, we prepared a bR photocell with a stripe-patterned bR thin film and measured its photocurrent response. The new patterning method is applicable to complicated patterning and patterning with a higher spatial resolution, which extends the application of bR thin films as sensor devices.