Nypa fruticans Wurmb. is one of the important underutilized fruit of Malaysia, which lacks scientific attention. Total phenolics, flavonoid content, and antioxidant capacities from endosperm extracts of Nypa fruticans (unripe and ripe fruits) were evaluated. Endosperm extract of unripe fruits (EEU) exhibited the highest phenolics (135.6 ± 4.5 mg GAE/g), flavonoid content (68.6 ± 3.1 RE/g), and antioxidant capacity. Free radical scavenging capacity of EEU as assessed by 2-2'-azino-bis (3-ethylbenz-thiazoline-6-sulfonic acid (ABTS) and 1,1-diphenyl-2-picryl hydrazyl (DPPH) radicals showed inhibitory activity of 78 ± 1.2% and 85 ± 2.6%, respectively. Beta carotene bleaching coefficient of EEU was higher (2550 ± 123), when compared to endosperm extract of ripe fruits (1729 ± 172). Additionally, EEU exhibited high antioxidant capacity by phosphomolybdenum method and ferric reducing antioxidant power values. Eight phenolic compounds from Nypa fruticans endosperm extracts were identified and quantified by ultra-high-performance liquid chromatography. Chlorogenic acid, protocatechuic acid, and kaempferol were the major phenolic compounds. Thus this fruit could be used as a potential source of natural antioxidant.