Functional lipids rich in ω?3 polyunsaturated fatty acids (ω?3PUFA) are widely used in food and medicine because of their special nutritional and physiological effects in brain function and vision development. Fish oil is the main source of ω?3PUFA. Lipases have been used as unique enzymatic tools to selectively prepare functional lipids, improve the structure of natural lipids and provide specific bioactivities, due to their efficient catalysis and selectivity. In this review, recent research progress on lipase catalysis used for fish oil processing was presented and discussed, analyzing the superiority of enzymatic catalysis in the production of health?promoting lipids enriched in ω?3PUFA in the formation of ethyl esters, 2?monoacylglycerols, structured triglycerides and structured phospholipids. The main factors, e.g., solvent composition and reaction conditions, on the esterification, transesterification and hydrolysis reactions catalyzed by lipase was also discussed in the production of ω?3PUFA?rich lipids. Finally, the main challenges in the application of enzymatic catalysis technique in the production of functional lipids from fish oil were summarized, and the crucial directions for future research in this field was proposed.