Fungal contamination of grains, intended for human and animal consumption, during the pre/post-harvest periods has been a recurring health hazard. A pulsed UV-light system was used to inactivate fungal spores of Aspergillus niger in corn meal. Response surface methodology was utilized for experimental design. The three process parameters evaluated were treatment time (20–100 s), voltage input (2000–3800 V), and distance from the UV strobe (3–13 cm). Optimization of the process parameters was validated by a quadratic regression equation designed to fit the experimental log10 reduction of fungal spores. Model prediction for a 100-s treatment time, 3 cm of distance from the UV strobe, and with 3800 V input gave a 4.93log10 reduction of A. niger. Modification of the pulsed UV-light system was recommended to maximize the UV fungal disinfection while minimizing the heat generation.