In this study antioxidant and anticancer effect of fucoidan isolated from brown seaweed Sargassum polycystum was investigated. The total yield of fucoidan was 4.51 ± 0.24%, of these, 46.8% of fucose and 22.35 ± 0.23% of sulphate respectively. The structural characteristic of fucoidan was analyzed by Fourier transform infrared spectroscopy and nuclear magnetic resonance. The antioxidant properties were determined by DPPH scavenging, reducing power and total antioxidant assays. The maximum DPPH scavenging activity (61.2 ± 0.33%), reducing ability (67.56 ± 0.26%) and total antioxidant activity (65.3 ± 0.66%) were obtained at 1000 μg/ml of fucoidan. The cytotoxicity effect of fucoidan showed a higher percentage (90.4 ± 0.25%) of inhibition against the MCF-7 cell line at 150 μg/ml with an estimated IC50 at 50 μg/ml. Further, cytomorphological and apoptosis changes of fucoidan treated cells were observed under inverted light microscope and confocal laser scanning microscope (CLSM). The results demonstrated that the isolated fucoidan from S. polycystum possessed potent antioxidant and anticancer properties.