BackgroundGlobally, three million girls are at risk of female genital mutilation (FGM) and an estimated 200 million girls and women in the world have undergone FGM. While the overall prevalence of FGM in Ghana is 4%, studies have shown that the overall prevalence in the Upper East Region is 38%, with Bawku municipality recording the highest at 82%.MethodsThis study used a cross-sectional design with a quantitative approach: a survey with women of reproductive age (15–49).ResultsAmong all respondents, 830 women who participated in the study, 61% reported having undergone FGM. Of those circumcised, 66% indicated their mothers influenced it. Three quarters of the women think FGM could be stopped through health education. Women who live in the Pusiga district (AOR: 1.66; 95% CI: 1.16–2.38), are aged 35–49 (AOR: 4.24; 95% CI: 2.62–6.85), and have no formal education (AOR: 2.78; 95% CI: 1.43–5.43) or primary education (AOR: 2.10; 95% CI: 1.03–4.31) were more likely to be circumcised relative to those who reside in Bawku Municipal, are aged 15–24, and had tertiary education. Likewise, married women (AOR: 3.82; 95% CI: 2.53–5.76) were more likely to have been circumcised compared with unmarried women. At a site-specific level, factors associated with FGM included age and marital status in Bawku, and age, marital status, and women’s education in Pusiga.ConclusionFemale Genital Mutilation is still being practiced in the Bawku Municipality and the Pusiga District of northern Ghana, particularly among women with low socio-economic status. Implementing interventions that would provide health education to communities and promote girl-child education beyond the primary level could help end the practice.