Unusual fatty acids with special carbon chain length or functional groups have been extensively used in the chemical, material, nutraceutical, and pharmaceutical industries. The traditional sources of these valuable fatty acids mainly include animal or plant extraction and chemical synthesis, which are unsustainable and may cause considerable environmental issues. The advancement of synthetic biology tools has facilitated the microbial production of lipids enriched in these fatty acids. The oleaginous yeast Yarrowia lipolytica is considered an attractive industrial host suitable for the production of advanced unusual fatty acids due to its high intrinsic lipogenesis ability. In this review, we introduce the most cutting-edge developments in synthetic biology tools for Y. lipolytica, as well as the recent progress in harnessing these tools to engineer the Y. lipolytica chassis to overaccumulate various unusual fatty acids, including odd-chain fatty acids, conjugated fatty acids, polyunsaturated fatty acids, cyclopropane fatty acids, methyl-branched fatty acids, hydroxylated fatty acids, and medium chain fatty acids. In addition, the future prospects of the unusual fatty acids using the Y. lipolytica platform are discussed in light of the current progress, challenges, and trends in this field. Finally, guidelines for future studies are also emphasized.