As Arctic ice recedes, future oil spills pose increasing risk to keystone species and the ecosystems they support. We show that Polar cod (Boreogadus saida), an energy-rich forage fish for marine mammals, seabirds, and other fish, are highly sensitive to developmental impacts of crude oil. Transient oil exposures =300 µg/L during mid-organogenesis disrupted the normal patterning of the jaw as well as the formation and function of the heart, in a manner expected to be lethal to post-hatch larvae. More importantly, we found that exposure to lower levels of oil caused a dysregulation of lipid metabolism and growth that persisted in morphologically normal juveniles. As lipid content is critical for overwinter survival and recruitment, we anticipate Polar cod losses following Arctic oil spills as a consequence of both near-term and delayed mortality. These losses will likely influence energy flow within Arctic food webs in ways that are as-yet poorly understood.