Moving-mask lithography with backside exposure was utilized to generate master male mold for biodegradable polymer microneedle production. The microneedle shape was calculated from the exposure dose, mask geometry, and moving trajectory using a newly developed computer simulation. Two conditions (90 µm aperture with 80 µm diameter of circular movement, and 90 µm aperture with 90 µm diameter of circular movement) were selected to evaluate the moving-mask exposure effectiveness. By changing the moving trajectory, two different sizes of microneedles were obtained from a single-size aperture mask. The fabricated microneedle and calculated microneedle geometry showed good qualitative agreement. The geometrical difference was 2% in basal diameter and 8%–16% in height. Using the master male mold, biodegradable polymer microneedles made of chondroitin sulfate C sodium salt (CSC) were fabricated by casting from a poly-dimethylsiloxane female mold. The shape of the biodegradable CSC microneedles showed good agreement with the master male mold.