Acoustic allometry occurs when features of animal vocalisations can be predicted from body size measurements. Despite this being considered the norm, allometry sometimes breaks, resulting in species sounding smaller or larger than expected. A recent hypothesis suggests that allometry-breaking animals cluster into two groups: those with anatomical adaptations to their vocal tracts and those capable of learning new sounds (vocal learners). Here we test this hypothesis by probing vocal tract allometry in a proven mammalian vocal learner, the harbour seal (Phoca vitulina). We test whether vocal tract structures and body size scale allometrically in 68 individuals. We find that both body length and body weight accurately predict vocal tract length and one tracheal dimension. Independently, body length predicts vocal fold length while body weight predicts a second tracheal dimension. All vocal tract measures are larger in weaners than in pups and some structures are sexually dimorphic within age classes. We conclude that harbour seals do comply with allometric constraints, lending support to our hypothesis. However, allometry between body size and vocal fold length seems to emerge after puppyhood, suggesting that ontogeny may modulate the anatomy-learning distinction previously hypothesised as clear-cut. Species capable of producing non-allometric signals while their vocal tract scales allometrically, like seals, may then use non-morphological allometry-breaking mechanisms. We suggest that seals, and potentially other vocal learning mammals, may achieve allometry-breaking through developed neural control over their vocal organs.