Diverse phycocyanin (PC) extraction and purification methods for cyanobacteria have been reported in literature. A particular method is not applicable to all cyanobacteria and the best method seems to be genus/species specific. Here, we report PC extraction and purification method for the filamentous cyanobacterium Anabaena fertilissima, a hyperproducer of phycobiliproteins. PC was also characterised in terms of unit assembly and stability. PC was extracted by freeze-thawing in distilled water, concentrated by ammonium sulphate fractionation and purified by size exclusion chromatography. The purification process resulted in 5.85-fold increase in PC purity reaching to 3.28. SDS-PAGE of purified PC demonstrated two bands of 19 and 21 kDa. Based on analysis of non-denaturing PAGE, the native PC from this organism is suggested to be a hexamer (αβ)₆ of 240 kDa. Lyophilised PC in powder form was more stable compared to PC in the solution. Half-life of dry PC is 110 days when stored at 4 °C in dark. Storage of PC in light at elevated temperature decreased its half life. When added to milk products, PC was stable up to 9 days when stored at 4 °C. Aqueous solution of PC also exhibited significant free radical scavenging activity. The PC from this organism has potential applications in food as a natural pigment and conservative due to its antioxidant properties.