Female genital mutilation has multiple adverse impacts on victims’ physical and psychosocial well-being. This study aimed to determine the prevalence and potential factors associated with female genital mutilation in Benin. A logistic regression was performed on the 2011 Benin Demographic and Health Survey dataset, using Stata 12. The dependent variable was based on participants’ declaration about the “Cut respondent’ question and was dichotomous (Yes/No). Independent variables were sociodemographic characteristics. A total of 11,008 women were selected, with 7.14% (CI 95% = [5.91, 8.60]) reported to be victims of female genital mutilation. The majority of the women were between 25 and 34 years old (34.5%), uneducated (54.6%), and married (51.3%). Women aged 35 to 49 were more likely to be victims of FGM than women aged 15 to 18 (OR = 5.43; CI 95% [3.77-7.82]). The risk of FGM was higher in married women (OR = 7.76) than those who had never been in a union, with the same trend observed for Muslim women (OR = 33.39) compared to followers of voodoo/traditional religion. Female genital mutilation is still practiced in Benin, especially in the north. This study reveals that factors such as marital status, religion, area of residence, level of education, ethnicity, and département of residence are associated with this practice. Therefore, they should be taken into account for effective interventions to eliminate it at national level.