Shielded Cs irradiators are routinely used in pre-clinical radiation research to perform in vitro or in vivo investigations. Without appropriate dosimetry and irradiation protocols in place, there can be large uncertainty in the delivered dose of radiation between irradiated subjects that could lead to inaccurate and possibly misleading results. Here, a dosimetric evaluation of the JL Shepard Mark I-68A Cs irradiator and an irradiation technique for whole-body irradiation of small animals that allows one to limit the between subject variation in delivered dose to ±3% are provided. Mathematical simulation techniques and Gafchromic EBT film were used to describe the region within the irradiation cavity with homogeneous dose distribution (100% ± 5%), the dosimetric impact of varying source-to-subject distance, and the variation in attenuation thickness due to turntable rotation. Furthermore, an irradiation protocol and dosimetry formalism that allows calculation of irradiation time for whole-body irradiation of small animals is proposed that is designed to ensure a more consistent dose delivery between irradiated subjects. To compare this protocol with the conventional irradiation protocol suggested by the vendor, high-resolution film dosimetry measurements evaluating the dose difference between irradiation subjects and the dose distribution throughout subjects was performed using phantoms resembling small animals. Based on these results, there can be considerable variation in the delivered dose of > ± 5% using the conventional irradiation protocol for whole-body irradiation doses below 5 Gy. Using the proposed irradiation protocol this variability can be reduced to within ±3% and the dosimetry formalism allows for more accurate calculation of the irradiation time in relation to the intended prescription dose.