The concentration of cortisol in hair (HCC) of polar bears (Ursus maritimus) may provide a retrospective view of physiological stress they experience and a link to their response to environmental change. To understand this relationship, we assayed HCC from polar bears captured in the Alaska Beaufort, Bering and Chukchi seas during 1983–1989 and 2004–2016. Cortisol accumulated in hair through summer and autumn and into the subsequent winter. HCC was similar between adult males and adult females. No difference in HCC across regions suggested all bears responded similarly to the environment. HCC in spring was elevated following years with a high winter Arctic Oscillation index and highly variable wind speed. HCC increased non-linearly with increasing duration of the continental shelf summer open water period up to 50 days and then decreased. HCC of spring samples declined with increasing body size, indicating that the stress response was more active in smaller bears or those in poor body condition. HCC of spring samples was greater and more variable in 2004–2006 than during either 1983–1989 or 2008–2016, and significantly so for females with 1st year cubs and subadult females. Elevated HCC in 2004–2006 coincided with years of reduced survival of southern Beaufort Sea polar bears and suggests that unidentified environmental perturbations impacted Alaska polar bears. Because HCC may be obtained by relatively non-invasive means, it has potential use for assessing polar bear populations that are difficult to study by capturing. Hence, information gained from HCC can inform polar bear conservation, especially on the vulnerability of subadult females and adult females with new cubs, and possible future environmental perturbations impacts on bear physiology.