This study aimed at valorisation of sea buckthorn pomace (SBP) for the production of extracts containing valuable bioactive compounds. For this purpose, SBP defatted by supercritical CO2 was subjected to consecutive fractionation with pressurized ethanol and water, which yielded 11.9% and 4.8% of extracts, respectively. The extracts were evaluated for their antioxidant potential, phytochemical composition and antiproliferative effects against cancer cells. Water extracts exhibited remarkably higher values in Folin-Ciocalteu assay of total phenolic content, oxygen radical absorbance capacity (ORAC), ABTS●+/DPPH● scavenging and cellular antioxidant activity (CAA) assays and more efficiently inhibited proliferation of HT29 cells at non-cytotoxic concentrations measured in non-tumoral Caco2 cells. Among 28 detected and 21 quantified phytochemicals, flavonols with the structures of isorhamnetin (five compounds), quercetin (three compounds), kaempferol (three compounds) glycosides and catechin (six compounds) were the most abundant in the extracts. In conclusion, the applied method of fractionation of SBP produces promising natural antioxidant complexes with antiproliferative properties that could find potential applications in nutraceuticals, functional foods and cosmeceuticals.