This study was aimed at the chemical profiling of flavonoid glycosides in antioxidant (AO) fractions of sea buckthorn (Hippophae rhamnoides) seed. Seed fractions were evaluated for their DPPH, ABTS, superoxide and hydroxyl radical scavenging, ferric reduction, ferrous chelation and xanthine oxidase inhibitory capacities. HPLC-DAD-ESI-MS/MS analytical conditions for the profiling of seed flavonoids were optimized and the AO-rich fraction was analysed. Quercetin-3-O-rutinoside (5.9%), isorhamnetin-3-O-rutinoside (4.9%) and isorhamnetin-3-O-sophroside-7-O-rhamnoside (3.7%) were found as the major flavonoid glycosides in the fraction. Significant amounts of isorhamnetin-3-O-glucoside (2.8%), 3-O-sophroside-7-O-rhamnosides of quercetin (2.4%) and kaempherol (1.3%), and 3-O-glucoside-7-O-rhamnosides of quercetin (1.1%) and isorhamnetin (1.1%) along with their free forms: isorhamnetin (2.7%), quercetin (1.1%) and kaempherol (0.6%) were also found in the fraction. The identification of flavonoids as the major less polar AO phenolics in the seeds was rationalized by demonstrating the high AO activity of isorhamnetin, quercetin, kaempherol and quercetin-3-O-rutinoside.