FA profiles of catfish liver oils were analyzed after microwave-assisted (without solvent extraction) and/or conventional (with solvent extraction) preparation methods. Microwave heating of the smaples was performed at 100, 80, 60, or 40% power at 1,000 W and 2,450 MHz, each for 80, 60, 40, or 20 s. Significant differences in the content of recovered FA were observed among the microwave-heated samples, except for C20∶0 and C20∶4. Recovery of C16∶0, C20∶0, and C20∶4 from the samples analyzed by the microwave-assisted method was lower than that of the samples analyzed by the conventional method. Much greater recovery was observed for C18∶1, C18∶2, and C22∶6; however, the recovery was not different from or was only slightly lower than that of the conventional method when microwave heating was set at 40% power for 20 s. This was also observed for the total unsaturated or saturated FA. Compared to other microwave treatments, heating at 100% power for 80 s yielded the greatest recovery of C14∶0, C18∶0, C18∶1, C18∶2, C18∶3, C20∶1, C20∶2, and C22∶6.