Sedentary behaviors and dietary intake are independently associated with obesity risk. In the literature, only a few studies have investigated gender differences for such associations. The present study aims to assess the association of sedentary behaviors and unhealthy foods intake with obesity in men and women in a comparative manner. The analysis presented in this study was based on the data from a population-based, cross-sectional, nationally representative survey (Indonesian Basic Health Research 2013/RISKESDAS 2013). In total, 222,650 men and 248,590 women aged 19–55 years were enrolled. A validated questionnaire, physical activity card, and food card were used for the assessments. The results showed that the prevalence of obesity (body mass index of ≥27.5 kg/m2) was higher in women (18.71%) than in men (8.67%). The mean body mass index in women tended to be higher than in men. After adjusting for age and education, the gender effect on obesity persisted in women and was more significant than in men. There was also a positive and significant effect on obesity of sedentary behaviors and unhealthy foods intake. Moreover, fatty and fried foods displayed a positive multiplicative interaction, increasing obesity risk in women more than in men and indicating a possible dietary risk in in women in relation to obesity. The study suggests that the implementation of educational programs on nutrition and physical activity is particularly important for promoting a healthy body weight among Indonesian women.