This study examined the potential of using the filamentous fungus Rhizopus oligosporus as a feedstock for hydrothermal liquefaction (HTL). The fungal biomass, cultivated in thin stillage from a corn ethanol plant, was processed at pilot-scale using a 1.5-L capacity continuous-flow HTL system. HTL operating conditions of 300–400 °C at 27 MPa for 12–30 min were tested. Biocrude yields ranging from 48.2 to 60.9% were obtained. At low reaction temperatures (300 °C), yields as high as 59.9% could still be achieved. Aside from the least severe reaction condition studied (300 °C, 12 min), neither the yield nor elemental composition of the biocrude was significantly impacted by residence time or temperature, as is typically seen with batch reactors. Similarities in the biochemical and elemental composition between R. oligosporus and microalgae resulted in biocrude yields that were comparable to those previously reported for continuous-flow systems using microalgae. These findings demonstrate the viability of using fungal biomass as a feedstock for the HTL process, and they show that lower temperatures can be used at pilot-scale while still achieving maximal yields.