Citrus fruit is important source of flavonoids, mainly flavanones which are narirutin and hesperidin. Those citrus flavonoids have been found to have health-related properties including antioxidant, anticancer, and anti-inflammatory. The main purpose of this study was to verify that the extraction of narirutin and hesperidin from Citrus peel can be more effective by combining pulsed electric field (PEF) pre-treatment and subcritical water extraction (SWE). Citrus unshiu peels were treated with PEF under conditions of electric field strength (3 kV/cm) and times (1 and 2 min). Subsequent SWE was conducted by using a Dionex Accelerated Solvent Extractor (ASE, Model 350) at extraction temperature 170°C for 10 min. The total flavonoids content was measured by using the aluminum chloride colorimetric method and the antioxidant capacity was analyzed by the Ferric reducing antioxidant power (FRAP) assay using spectrophotometer. The concentrations of narirutin and hesperidin were increased as PEF pre-treatment time increased. The highest concentrations of narirutin and hesperidin were 13.41 mg narirutin/g dry citrus peel and 141.16 mg hesperidin/g dry citrus peel at PEF pre-treatment condition of 3 kV/cm and 2 min. The total flavonoids contents of the extracts increased 105.2% and 123.1% for citrus peel PEF treated at 1 and 2 min, respectively. In addition, compared to the untreated sample, PEF pre-treatments of 1 and 2 min increased the antioxidant capacity of the extracts 109.2% and 160.8%, respectively. Therefore, the results demonstrate the potential of PEF pre-treatment to improve the SWE of flavonoids from citrus unshiu peel.