Abstract Microalgae have been proposed as potentially promising feedstock for the production of renewable transportation fuels. The plants are intriguing for their capacity to serve both as a source of renewable carbon fuels and as a powerful tool for carbon sequestration. Microalgae remnant, a low-cost by-product of microalgae lipid extraction, is a particularly appealing candidate for these processes. Through catalytic pyrolysis, microalgae remnant is capable of producing aromatic hydrocarbons that could be used for the production of drop-in biofuels. One of the most challenging barriers to this promising pathway is the high moisture content of harvested microalgae. The goal of this study is to compare the economics of two catalytic pyrolysis pathways for the production of drop-in biofuels, each pathway employing its own distinct method of feedstock dewatering: thermal drying or partial mechanical dewatering. The study presents chemical process models, capital expense and operating cost estimates, and sensitivity analyses of both scenarios. Results indicate that thermal drying prior to catalytic pyrolysis (TDCP) incurs capital costs similar to those incurred in partial mechanical dewatering prior to catalytic pyrolysis (MDCP) ($346 million vs. $409 million). TDCP and MDCP yield minimum fuel-selling prices (MFSPs) of $1.80/l and $1.49/l, respectively. Energy analysis shows that TDCP achieves 16.8% energy efficiency and MDCP achieves 26.7% efficiency.