Modern small animal irradiation platforms provide for accurate delivery of radiation under 3D image guidance. However, leveraging these improvements currently comes at the cost of lower-throughput experimentation. Herein, we characterized setup accuracy and dosimetric robustness for mock/sham irradiation of a murine xenograft flank tumor model using the X-RAD SmART+ with the vendor-supplied Monte Carlo (MC) treatment planning system (SmART ATP). The chosen beam arrangement was parallel-opposing using a 20 mm square collimator, aligned off-axis for ipsilateral lung sparing. Using a cohort of five mice imaged with cone beam computed tomography (CBCT) over five consecutive mock-irradiation fractions, we compared inter-fraction setup variability resulting from a vendor-supplied multi-purpose bed with anesthesia nose cone with a more complicated immobilization solution with an integrated bite block with nose cone and Styrofoam platform. A hypothetical “high-throughput” image-guidance scenario was investigated, wherein the day 1 stage coordinates (resulting from CBCT guidance) were applied on days 2–5. Daily inter-fraction setup errors were evaluated per specimen (days 2–5) using CBCT-derived offsets from day 1 stage coordinates. Using the CBCT images and Monte Carlo dose calculation, 3D dosimetric plan robustness was evaluated for the vendor-supplied immobilization solution, for both the high-throughput guidance scenario as well as for use of daily CBCT-based alignment. Inter-fraction setup offset magnitude was 3.6 (±1.5) mm for the vendor-supplied immobilization compared to 3.3 (±1.8) mm for the more complicated solution. For the vendor-supplied immobilization, we found that daily CBCT was needed to adequately cover the flank tumors dosimetrically, given our chosen treatment approach.