Incorporation of capric acid (CA) into arachidonic acid (AA) single-cell oil, using five commercial lipases, indicated that lipase PS-30 from Pseudomonas sp. was most effective. The optimal conditions included an oil-to-CA mole ratio of 1∶3, a temperature of 45°C, incubation time of 24 h, 4% lipase from Pseudomonas sp., and a 2% (w/w) water content. Examination of positional distribution of FA on the glycerol backbone of modified AA single-cell oil with CA showed that 89.7% of CA was concentrated in the sn-1,3 positions of the TAG molecules. AA was mainly located at the sn-2 position of the modified AA single-cell oil. Enzymatically modified AA single-cell oil had a higher conjugated dienes (CD) value than its unmodified counterpart. TBARS values of both modified and unmodified AA single-cell oils increased progressively during the entire storage period, but no significant difference existed between TBARS values of both oils. Thus, enzymatically modified oil was more susceptible to oxidation than its unmodified counterpart, when considering both CD and TBARS values. Removal of natural antioxidants during oil modification might play a significant role in rapid oxidative deterioration of enzymatically modified oils. This possibility was confirmed when starting materials were subjected to the same reaction process in the absence of any enzyme, as the resultant oil was indeed significantly less stable than the control oil.