The ejection fraction of the trabeculated cardiac ventricle of reptiles has not previously been measured. Here, we used the gold standard clinical methodology – electrocardiogram-gated flow magnetic resonance imaging (MRI) – to validate stroke volume measurements and end diastolic ventricular blood volume. This produced an estimate of ejection fraction in our study species, the red footed tortoise Chelonoidis carbonarius (n=5), under isoflurane anaesthesia of 88±11%. After reduction of the prevailing right-to-left intraventricular shunt through the action of atropine, the ejection fraction was 96±6%. This methodology opens new avenues for studying the complex hearts of ectotherms, and validating hypotheses on the function of a more highly trabeculated heart than that of endotherms, which have lower ejection fractions.