Measurements obtained from aerial imagery can be used to calculate body shape, condition and growth rates of large surface-associated marine megafauna. In this study, an unoccupied aerial vehicle (UAV) was used to obtain aerial images of an elasmobranch species, the whale shark (Rhincodon typus). Pre-caudal length (PCL) and multiple body width measurements were taken from aerial images of 26 juvenile whale sharks, obtained between November 2020 and February 2021 in the La Paz Bay, Mexico. PCL ranged from 2.98 to 6.43 m, with a mean of 4.93 m (SD = 1.00). Body width was found to be greatest in the region by the snout and anterior contacts of the pectoral fins. Body width decreased in a near-linear manner from ~ 18% PCL at the midpoint to ~ 10% PCL at the posterior end of the body. There was a significant linear relationship between whale shark dorsal surface area (SA) and PCL on the log–log scale (LM: F1,24 = 647.7, P < 0.001), showing that whale sharks increase exponentially in overall body size as they increase in body length. However, there was no effect of PCL on the relative body width at the different measurement sites, suggesting that body shape of whale sharks was similar across the size range measured in this study. Finally, the body condition of the sharks, measured as the residual of the relationship between SA and PCL, varied between − 21.6% and + 14.0%. This study highlights the benefits of using UAV photogrammetry to measure large marine fauna, to obtain valuable morphometric data to study their physiology and bioenergetics.