In the Arctic, winter warming and loss of sea ice pose largely unknown risks to keystone species and the marine ecosystem that they support. Young-of-the-year juvenile polar cod, Boreogadus saida, are an energy-rich forage fish that accumulate high levels of lipid in the summer but retain a relatively small body size during the winter. To address winter bioenergetics and survival, we held age-0 juveniles under simulated winter conditions (food deprived, 24-hr darkness) at a range of four constant temperatures (−1, 1, 3, 5 °C). Our goals were to 1) determine how age-0 polar cod utilize lipid energy in muscle and liver across variable temperatures and durations of food deprivation, 2) understand temperature- and size-dependent impacts on survival and 3) provide energy loss models using multiple condition metrics that are commonly used in fisheries science (lipids, morphometric ratios, body weight). These data have relevance to projecting winter outcomes for polar cod sampled pre-winter, when fish are more easily sampled in the field. As expected, in the absence of food, juvenile polar cod better conserved lipids and survived longer at colder temperatures. There was no negative impact of cold extremes on this pattern; for example, 50% mortality was at 170 days when polar cod were held at −1 °C, compared to only 94 days when they were held at 5 °C. During the first 28 days of simulated winter, polar cod preferentially catabolized triacylglycerols from muscle tissue, then depleted this storage lipid class in their muscle and liver until starvation. Mortality occurred when whole-body lipid concentrations fell below 12.4 mg g−1 wet weight. Temperature-dependent declines in morphometric condition (hepatosomatic index and Fulton's K) and lipid content were parameterized and developed into temperature-dependent condition loss models. Applying a laboratory-based lipid loss model to field-collected polar cod demonstrated that winter survival is highly sensitive to small changes in temperature between −1 and 1 °C when fish are in good condition at the end of the preceding summer. Alternatively, fish in poor summer condition cannot survive winter relying exclusively on stored energy reserves, and will be required to forage throughout the winter. Collectively, these results suggest that lipid-based indices offer a sensitive means of predicting overwintering success for polar cod experiencing climate-driven changes in summer and winter habitats in the Arctic.