Body size affects almost every aspect of the biology of a species, with considerable intraspecific variation. Cheetahs (Acinonyx jubatus) reportedly vary in body size across their geographical range. However, because morphometric measurements were not taken in a standardized manner, it is impossible to rule out differences in measurement protocols as the cause. Our study differed from previous ones in that we made use of a standardized methodology for taking morphometric measurements in cheetahs. Free-ranging cheetahs in Namibia were shorter (3.5–4.1%) and slimmer (4.0–7.0%) than those in neighboring Botswana. Cheetah density was more than 3 times higher and home-range sizes were more than 3 times smaller in Botswana compared to Namibia. This suggests that variation in resource availability may be the main driver of the fine-scale spatial differences in morphometric measurements. Overall, our study promotes the use of standardized protocols for measuring morphological traits in free-ranging animals.