Fabrication of the catalytic layers in polymer electrolyte fuel cells (PEFCs) typically involves a powder-film drying process, in which material ink is prepared, coated, and then dried. The process exhibits complex phenomena and requires adjustments of a huge number of parameters to control each phenomenon. We applied Bayesian optimization to determine the temperature profile during the drying process, to obtain electrodes with smooth surfaces. The results suggest that pulsed heat treatments were more effective in smoothening of surface than in maintaining a low temperature. Further, we investigated the effect of pulsed heat treatments and discussed the mechanism of ink drying.