Lipids from pumpkin seeds, has been widely used in the treatment of prostatic hyperplasia attributed due to its high content in unsaturated fatty acids like linoleic, oleic, palmitic and estearic as the main active principles. This study deals with the optimization of microwave assisted extraction (MAE) of lipids from Cucurbita pepo L. seeds. To evaluate the effect of three independent variables, etanol to plant material ratio, microwave power used for extraction and Irradiation time, Box–Behnken design of Response surface methodology has been employed. The design model estimated the optimum yield of 19,89% at 900 W microwave power level, 10 mL/g solvent to plant material ratio and 54 seconds of irradiation time. In comparison with the conventional solvent extraction by reflux, the MAE is 37 times faster and with a significant saving of solvent. However, the lipids compositions in extracts by both methods were similar, which were investigated using FTIR and Gas Chromatography.