Although hypertension is among the main public health concerns in Indonesia, due to the scarcity of data, few studies have investigated the factors associated with hypertension in men and women. This study aimed to examine the prevalence of and factors associated with hypertension among adult men and women in Indonesia. The 2018 Survey of the Sleman Health Demographic and Surveillance System was utilized, consisting of 4328 individuals aged 18+ years. Multivariable logistic regression analysis was performed to determine the sociodemographic and health behavior factors of hypertension. Overall, the prevalence of hypertension was 40% (42% in men and 38% in women). Age, abdominal obesity and chronic non-communicable diseases were the common predictors of hypertension in men and women (p < 0.05). The odds ratio of hypertension among men with low education was lower than among those with high education (OR = 0.52, 95% CI: 0.29–0.94). For women, being in the poorest socioeconomic condition increased the risk of hypertension by 1.67 times compared to the richest (95% CI: 1.21–2.32). Gender differences in the prevalence of and factors associated with hypertension were observed among adult populations in Sleman District, Yogyakarta, Indonesia. Therefore, a gender-based approach in the health prevention strategy to control hypertension for men and women is needed.