In this study, pumpkin seed oil was microencapsulated by spray-drying for stabilization of oil quality during the storage. Different carbohydrates including gum arabic, modified corn starch, modified manioc starch, maltodextrin, sucrose, maltose, lactose and glucose were alternatively combined with whey protein isolate for microencapsulation of pumpkin seed oil. Mixture of whey protein and maltodextrin generated the spray-dried powder with high microencapsulation efficiency as well as high microencapsulation yield. This wall system also produced the powder with the lowest peroxide value at the end of the acceleration storage. The appropriate whey protein/maltodextrin ratio was 1/3 under which the microencapsulation efficiency and yield for pumpkin seed oil were 94.5% and 65.6%, respectively. Microencapsulation was a potential method for protection of pumpkin seed oil against deterioration.