Inuit in Canada have high selenium intake from the consumption of country food such as fish and marine mammals. The health consequence is not known. This study examines the association between blood selenium concentration and prevalence of stroke among Canadian Inuit. The International Polar Year Inuit Health Survey was conducted in 2007–2008. Among the 2077 adults participants (≥18 years old) who completed a questionnaire and gave blood samples, 49 stroke cases were reported, 31 of which were from women. The crude prevalence of stroke was 2.4% in the participants. Participants with stroke had lower blood selenium (geometric mean: 260 μg/L vs. 319 μg/L) and dietary selenium (144 μg/day vs. 190 μg/day) compared to individuals without stroke. Participants with high blood/dietary selenium exposure (quartiles 3 and 4) had a lower prevalence of stroke compared to those with low selenium exposure (quartile 1). The adjusted odds ratio ranged from 0.09 to 0.25 among subgroups (e.g. age, sex, and blood mercury). An L-shaped relationship between prevalence of stroke with blood and dietary selenium was observed, based on the cubic restricted spline and segmented regression analyses. The estimated turning points of the L-shaped curve for blood selenium and dietary selenium were 450 μg/L and 350 μg/day, respectively. Below the turning points, it was estimated that each 50-μg/L increase in blood selenium was associated with a 38% reduction in the prevalence of stroke, and each 50-μg/day increase in dietary selenium was associated with a 30% reduction in the prevalence of stroke. In conclusion, blood and dietary selenium are reversely associated with the prevalence of stroke in Inuit, which follows an L-shaped relationship. Whether this relationship applies to other population needs further investigation.