Herein we demonstrated an economically beneficial process coproducing biojet fuel and high-value polyunsaturated fatty acids (PUFAs) from Schizochytrium sp. ABC101 microalgae. Schizochytrium is a promising biofuel source for its rapid growth, high cell density, and fast lipid accumulation via heterotrophic cultivation. The most important feature of Schizochytrium is that half of its lipids are composed of omega-3 PUFAs (i.e., docosahexaenoic acid and docosapentaenoic acid), which are currently commercialized as dietary supplements at a high price. We observed direct injection of PUFA-rich lipid into a high-temperature catalytic reactor can cause rapid catalyst deactivation via coke deposition. Therefore, the PUFAs were separated by short-path distillation after transesterification. The remaining esters of saturated fatty acids (SFAs) were catalytically deoxygenated into C13–C18 n-paraffins, and then subsequently hydrocracked to produce iso-rich paraffins that are suitable as biojet fuel. As the result, 54.6 wt% PUFA-enriched esters (purity: 87.7%) and 20.4 wt% of qualified biojet fuel with respect to the initial lipids were obtained.