Fish oil was extracted from Euthynnus affinis whole fish captured from Red Sea, Egypt using conventional wet rendering method. Ecofriendly chitosan in a non‐centrifuged sequential purification (C/O‐NCSP) technique was employed to purify the resulting crude oil. Three different chitosan/oil ratios were investigated (2, 3, and 5% w/v) and the results revealed that chitosan/oil ratio; 5% w/v was the most efficient in the oil purification procedure with regards to protein, ash, water, heavy metal, and fatty acid content. The purification results obtained suggest that C/O‐NCSP (5% w/v) may be used as a potential commercial filter to get a good quality fish oil. Practical applications Kawakawa (Euthynnus affinis) fish has been known as a very common protein source of Egyptian diet. Kawakawa can contribute significantly in the Egyptian economy because fish farmers, fish processing industry as well as the pharmaceutical companies can benefit from Kawakawa fish as a source of oil for human consumption. Thus, the purification procedures must be chemically and environmentally safe. In the present study, green purification method is proposed for extracted crude oil from whole fish of Kawakawa using high viscosity chitosan polymer. The physical and chemical characteristics of purified crude oil were analyzed and evaluated. The proposed chitosan purification technique offered better quality fish oil for industrial applications. Thus, the outcomes of the present study can provide a replacement to traditional fish oil purification steps due to less chemical treatments during processing that could reduce effluents and this might help with the economic viability and quality of the end product.