The intake of polyunsaturated fatty acids especially omega-3 is projected to be way below the recommended intake in Kenya. Thus, there is need to find other sources of polyunsaturated fatty acids (PUFAs). This study screened for the lipid profile and levels of omega-3 PUFAs in jackfruit and explored the variation in lipid profile of jackfruit seeds in different areas and treatments. The extracted lipids were characterized and analysis done using gas chromatography. The lipid content was found to be 0.45 ± 0.24%, iodine number was 60.76 ± 3.25, saponification number was 353.65 ± 14.21, and levels of omega-3 and of omega-6 PUFAs were also found to be 9.94 ± 0.99% and 31.19 ± 0.82%, respectively. Boiling and drying of seeds were found to greatly decrease the levels of polyunsaturated fatty acids such omega-3 and omega-6 and thus, not suitable methods for processing or preservation of jackfruit seeds.