Cooking process is one of the most energy and time consuming steps in the edible oil extraction factories. The main goal of this study was cottonseed oil extraction by microwave radiation and elimination of any heat treatment of cottonseeds before extraction. The effect of cooking process on the physicochemical properties of extracted oil from two varieties of cottonseed (Pak and Sahel) was evaluated by free fatty acid content, melting point, smoke point and refractive index. Our results didn’t show any significant differences between cooked and uncooked samples (P > 0.05) regarding physicochemical characteristics. From GC analysis of extracted oils, it was found there is no significant difference in fatty acid composition of cooked, uncooked and control (conventional extraction) samples. The thermal stability (Rancimat) analysis of oil samples showed the cooking process could cause a slight increase in the stability of oils for both varieties (about 40 min). The cooking process also increased total extracted phenolic compounds and considerably decreased total gossypol content of the cottonseed oil; but the extraction efficiency didn’t change considerably after elimination of the cooking process. It can be concluded that microwave rays can destroy the structure of oil cells during process and facilitate the oil extraction without any heat treatment before extraction.