Subcritical water extraction (SCWE) is a modern extraction technique that provides a number of advantages compared with traditional solvent extraction methods. The use of water rather than solvents is particularly advantageous when extracting medically and commercially important phenolic compounds from food and food-processing by-products. In this study, SCWE was used to recover bioactive phenolic compounds from onion skins. The efficiency of extraction using the SCWE process was affected by extraction temperature, particle size and pH. Extraction temperature was found a key factor affecting total phenolic content (TPC) and maximum TPC values were obtained at lower temperature. The antioxidant activity and total flavonoid content (TFC) of the extracts were mainly affected by the pH. Maximum antioxidant activity and TFC were obtained at higher pH during SCWE. Comparison of SCWE with conventional solvent extraction using ethanol also showed that subcritical water can be an excellent substitution for organic solvent when extracting bioactive compounds from onion skin.