Abstract Background and Aims Canada has one of the highest inflammatory bowel disease (IBD) incidence rates worldwide. Higher IBD incidence rates have been identified among urban regions compared to rural regions. The study objectives were to (i) estimate IBD incidence rates in Saskatchewan from 1999 to 2016 and (ii) test for differences in IBD incidence rates for rural and urban regions of Saskatchewan. Methods A population-based study was conducted using provincial administrative health databases. Individuals aged 18+ years with newly diagnosed Crohn’s disease or ulcerative colitis were identified using a validated case definition. Generalized linear models with a negative binomial distribution were used to estimate incidence rates and incidence rate ratios (IRRs) adjusted for age group, sex and rurality with 95% confidence intervals (CIs). Results The average annual incidence rate of IBD among adults in Saskatchewan decreased from 75/100,000 (95% CI 67 to 84) in 1999 to 15/100,000 (95% CI 12 to 18) population in 2016. The average annual incidence of IBD declined significantly by 6.9% (95% CI −7.6 to −6.2) per year. Urban residents had a greater overall risk of IBD (IRR = 1.19, 95% CI 1.11 to 1.27) than rural residents. This risk difference was statistically significant for Crohn’s disease (IRR = 1.25, 95% CI 1.14 to 1.36), but not for ulcerative colitis (IRR = 1.08, 95% CI 0.97 to 1.19). Conclusions The incidence of IBD in Saskatchewan dropped significantly from 1999 to 2016 with urban dwellers having a 19% higher risk of IBD onset compared to their rural counterparts. Health care providers and decision-makers should plan IBD-specific health care programs considering these specific IBD rates.