Response surface methodology was employed to optimize the extraction of apple pomace phenolics with water. The constructed models were adequate to explain the behavior of the extraction system and predict the responses, total phenolics, and 5-hydroxymethylfurfural. Among the studied factors, temperature, extraction time, and solvent to solid ratio had the greatest influence on the responses. Water extraction using a combination of 100 °C for temperature, 37 min for extraction time, and 100 mL/g for solvent to solid ratio provided an opportunity to extract the antioxidants of apple pomace by limiting the formation of 5-hydroxymethylfurfural. Twenty-nine phenolic compounds were characterized in apple pomace by HPLC-MS. Phenolic content of apple pomace was 8341 mg/kg of dry matter at optimized conditions, which offer an alternative, safer way to extract antioxidants than by use of organic solvents.