The aim of this study was to determine and compare the prevalence of pre-diabetes and type 2 diabetes mellitus (T2DM) among Sami and non-Sami men and women of rural districts in Northern Norway. The SAMINOR 2 Clinical Survey is a cross-sectional population-based study performed in 2012–2014 in 10 municipalities of Northern Norway. A total of 12,455 Sami and non-Sami inhabitants aged 40–79 years were invited to participate and 5878 were included in the analyses. Participants with self-reported T2DM and/or a glycated haemoglobin (HbA1c) result ≥6.5% were categorised as having T2DM. Those with 5.7%≤HbA1c<6.5% were categorised as pre-diabetics. In men, the total age-standardised prevalence of pre-diabetes (37.9% vs 31.4%) and T2DM (10.8% vs 9.5%) were higher in Sami compared with non-Sami; the ethnic difference was statistically significant for both pre-diabetes (OR 1.42, p < 0.001) and T2DM (OR 1.31, p = 0.042). In women, pre-diabetes (36.4% vs 33.5%) and T2DM (8.6% vs 7.0%) were also more common in Sami than non-Sami; the differences in both pre-diabetes (OR 1.20, p = 0.025) and T2DM (OR 1.38, p = 0.021) were also statistically significant. The observed ethnic difference in the waist-to-height ratio (WHtR) was a plausible explanation for the ethnic difference in the prevalence of pre-diabetes and T2DM.