Insulin resistance (IR) is defined as the subnormal response to insulin action on its target tissues. Studies suggest that IR may increase the risk of hypertension, but the results are inconsistent and it is not known whether such an effect is independent of overweight/obesity. We aimed to evaluate the association between IR and the incidence of prehypertension and hypertension in the Brazilian population and whether this association is independent of overweight/obesity. In 4717 participants of the Brazilian Longitudinal Study of Adult’s Health (ELSA-Brasil), free of diabetes and cardiovascular disease at baseline (2008–2010), we investigated the incidence of prehypertension and hypertension after a mean follow-up of 3.8 ± 0.5 years. Insulin resistance at baseline was assessed by the Homeostasis Model Assessment of Insulin Resistance (HOMA-IR) index, defined if above the 75th percentile. The risk of IR-associated prehypertension/hypertension was estimated by multinomial logistic regression after adjustment for confounding factors. Secondary analysis were stratified by body mass index. The mean (SD) age of participants was 48 (8) years, 67% were women. The 75th percentile of HOMA-IR at baseline was 2.85. The presence of IR increased the chance of developing prehypertension by 51% (95% CI 1.28–1.79) and hypertension by 150% (95% CI 1.48–4.23). In individuals with BMI < 25 kg/m2, the presence of IR remained associated with the incidence of prehypertension (OR 1.41; 95% CI 1.01–1.98) and hypertension (OR 3.15; 95% CI 1.27–7.81). In conclusion, our results suggest that IR is a risk factor for hypertension, regardless of the presence of overweight or obesity.