Tungsten trioxide (WO3) is a promising candidate as a photocatalyst because of its outstanding electrical and optical properties. In this study, we prepare WO3 thin films by electrodeposition and characterize the photocatalytic degradation of methylene blue using these films. Depending on the voltage conditions (static and pulse), compact and porous WO3 films are fabricated on a transparent ITO/glass substrate. The morphology and crystal structure of electrodeposited WO3 thin films are investigated by scanning electron microscopy, atomic force microscopy, and X-ray diffraction. An application of static voltage during electrodeposition yields a compact layer of WO3, whereas a highly porous morphology with nanoflakes is produced by a pulse voltage process. Compared to the compact film, the porous WO3 thin film shows better photocatalytic activities. Furthermore, a much higher reaction rate of degradation of methylene blue can be achieved after post-annealing of WO3 thin films.