Allocation of energy to thermoregulation greatly contributes to the metabolic cost of endothermy, especially in extreme ambient conditions. Weddell seal (Leptonychotes weddellii) pups born in Antarctica must survive both on ice and in water, two environments with very different thermal conductivities. This disparity likely requires pups to allocate additional energy toward thermoregulation rather than growth or development of swimming capabilities required for independent foraging. We measured longitudinal changes in resting metabolic rate (RMR) for Weddell seal pups (n=8) in air and water from one to seven weeks of age, using open-flow respirometry. Concurrently, we collected molt, morphometric and dive behavior data. Absolute metabolic rate (MR) in air followed the expected allometric relationship with mass. Absolute MR in water was not allometric with mass, despite a 3-fold increase in mass between one and seven weeks of age. Developmental stage (or molting stage), rather than calendar age, determined when pups were thermally capable of being in the water. We consistently observed post-molt pups had lower RMR in air and water (6.67±1.4 and 7.90±2.38 ml O2 min−1 kg−1, respectively) than pre-molt (air: 9.37±2.42 ml O2 min−1 kg−1, water: 13.40±3.46 ml O2 min−1 kg−1) and molting pups (air: 8.45±2.05 ml O2 min−1 kg−1, water: 10.4±1.63 ml O2 min−1 kg−1). RMR in air and water were equivalent only for post-molt pups. Despite the increased energy cost, molting pups spent three times longer in the water than other pups. These results support the idea of an energetic trade-off during early development; pups expend more energy for thermoregulation in water, yet gain experience needed for independence.