The Nigerian national control programme (NCP) for schistosomiasis does not have a specific action plan for female genital schistosomiasis (FGS), mainly due to gaps in epidemiological and clinical surveillance. To address this, we conducted a pilot investigation for FGS in girls (>5 and ≤15 years) and adult women (≥16 years) in four rural communities near Abeokuta, Ogun State. Urine samples were collected from 317 participants [children (n = 187), adults (n = 130)] and examined for ova of Schistosoma haematobium by microscopy. A total of 149 participants (47·0%) had egg-patent urogenital schistosomiasis [children (64·7%), adults (21·6%)], reported blood in urine was common (44·5%) as well as sign-post symptoms of FGS. To verify FGS directly, 20 adult women each underwent a gynaecological investigation by colposcopy with observed lesions classified according to the WHO FGS pocket atlas. Fourteen (70·0%) women presented with FGS as grainy-sandy patches (n = 10), homogenous yellow sandy patches (n = 6), nabothian cysts and rubbery papules (n = 1). Our study confirms FGS in Ogun State and calls for further appraisals of this disease in other areas where urogenital schistosomiasis is endemic. The Nigerian NCP should be encouraged to develop an appropriate response to FGS not only to detect it, but also to prevent it.