An apparatus for manufacturing a gas diffusion layer for fuel cells includes: a conveyer transferring a base sheet for a macroporous layer of the gas diffusion layer in one direction before water repellent coating; a nozzle disposed around the conveyer to coat the transferring base sheet with a water repellent in a fiber type or desired pattern; and a nozzle transfer unit combined with an upper end of the nozzle to transfer the nozzle along a desired trajectory.