Understanding the ontogeny of diving behaviour in marine megafauna is crucial owing to its influence on foraging success, energy budgets, and mortality. We compared the ontogeny of diving behaviour in two closely related species—northern elephant seals (Mirounga angustirostris, n = 4) and southern elephant seals (Mirounga leonina, n = 9)—to shed light on the ecological processes underlying migration. Although both species have similar sizes and behaviours as adults, we discovered that juvenile northern elephant seals have superior diving development, reaching 260 m diving depth in just 30 days, while southern elephant seals require 160 days. Similarly, northern elephant seals achieve dive durations of approximately 11 min on their first day of migration, while southern elephant seals take 125 days. The faster physiological maturation of northern elephant seals could be related to longer offspring dependency and post-weaning fast durations, allowing them to develop their endogenous oxygen stores. Comparison across both species suggests that weaned seal pups face a trade-off between leaving early with higher energy stores but poorer physiological abilities or leaving later with improved physiology but reduced fat stores. This trade-off might be influenced by their evolutionary history, which shapes their migration behaviours in changing environments over time.