Microbeam radiation therapy (MRT) is a pre-clinical, spatially-fractionated treatment modality noted for its ability to achieve a large differential response between normal and tumoral tissues. In the present study, TOPAS Monte Carlo (MC) simulations were used to optimize the design of a compact, affordable multi-slit collimator (MSC) suitable for use with the small animal radiation research platform (SARRP). MRT dose distributions in a (1  ×  1  ×  3)cm water phantom were simulated for a tungsten MSC using different focal spot sizes (0.4, 3 mm), beam energies (40, 80, 220 kVp), slit widths (100, 125, 150, 175, 200 µm), collimator thicknesses (1.5, 2.5, 3 cm) and collimator-to-surface distances (CSD of 1 and 3 cm). Key MRT figures of merit, namely the peak-to-valley dose ratio (PVDR), full-width at half-maximum and peak dose rate were determined. Use of the small focal spot maximized the PVDR (~40 at surface) and reduced the system's sensitivity to changes in CSD, but decreased the collimated beam output to 55.2 cGy min. The large focal spot was ill-suited for large CSD irradiations, but increased the beam output by a factor of 2.8, to 153.0 cGy min, and decreased the sensitivity to changes in slit width. A modular MSC, using divergent plastic spacer materials in place of excavated slits, was also investigated. Polypropylene and polyethylene terephthalate material spacers were considered and while neither reduced the PVDR compared to air slits, the dose rate was reduced by 37% and 47%, respectively. Lastly, a steel parallel-slit MSC was used in a preliminary test of MRT delivery using the SARRP. Discrepancies between the results of film dosimetry and the corresponding MC simulations highlight the need to fabricate a more well-defined collimator for use in future validation and radiobiological work. The simulated results of this study are being used to inform the design of such a collimator, which will additionally boast a high degree of modularity at reasonable cost.