Akebia trifoliata is a fruit with rich nutritional properties, and its peel is produced as a by-product. In this research, we investigated the influences of microwave-assisted extraction parameters on antioxidant activity of the extract from Akebia trifoliata peels, and the ferric-reducing antioxidant power (FRAP) and Trolox equivalent antioxidant capacity (TEAC) as well as total phenolic contents (TPC) were used to optimize extraction parameters. The influences of ethanol concentration, microwave power and solvent-to-material ratio, as well as extraction temperature and time on TPC, FRAP and TEAC values, were assessed using single-factor tests. Three parameters with obvious effects on antioxidant capacity were selected to further investigate their interactions by response surface methodology. The optimal extraction parameters of natural antioxidants from Akebia trifoliata peels were ethanol concentration, 49.61% (v/v); solvent-to-material ratio, 32.59:1 mL/g; extraction time, 39.31 min; microwave power, 500 W; and extraction temperature, 50 °C. Under optimal conditions, the FRAP, TEAC and TPC values of Akebia trifoliata peel extracts were 351.86 ± 9.47 µM Fe(II)/g dry weight (DW), 191.12 ± 3.53 µM Trolox/g DW and 32.67 ± 0.90 mg gallic acid equivalent (GAE)/g DW, respectively. Furthermore, the main bioactive compounds (chlorogenic acid, rutin and ellagic acid) in the extract were determined by high-performance liquid chromatography. The results are useful for the full utilization of the by-product from Akebia trifoliate fruit.