Intraspecific variation in cetacean vertebral anatomy as a result of ageing, growth, and sexual dimorphism is poorly understood. Using 3D geometric morphometrics, we investigated allometric patterns, sexual dimorphism, and ontogenetic trajectories in the vertebral column of false killer whale (Pseudorca crassidens). Our data set includes thoracic, lumbar, and caudal vertebrae of 30 specimens, including neonates, juveniles, and adults of both sexes. Vertebral shape was significantly correlated with size within each region. Neonatal vertebral shape differed significantly from juveniles and adults, displaying ontogenetic shape change. Allometric and growth patterns of the vertebral regions, particularly of the lumbar region with the thoracic and caudal regions, differed significantly, which may influence the function and mobility patterns of the vertebral regions during different life stages. Using quantitative methods, we could not conclude that the Pseudorca vertebrae are sexually dimorphic. This study describes for the first time intraspecific vertebral patterns in a cetacean species across ontogenetic stages. Pseudorca individuals live in large pods and swim together, sharing the same swimming mode. The neonates have a more flexible column and swim less efficiently following their mothers to nurse.