Female Genital Schistosomiasis is a gynecological disease that is a complication of parasitic Schistosoma haematobium infection and affects at least 40 million girls and women, mostly in sub-Saharan Africa. Little is known about how healthcare workers in endemic areas perceive and manage (diagnose and treat) Female Genital Schistosomiasis. We conducted cross-sectional focus group discussions and key informant interviews among healthcare workers in northwestern Tanzania. Healthcare workers, particularly those working in areas where S. haematobium is highly endemic, were purposively sampled to participate in the study. Discussions and interviews were digitally recorded, transcribed, and analyzed using NVivo version 12. Most healthcare workers lacked knowledge and skills to manage Female Genital Schistosomiasis. They also had multiple misconceptions about its aetiology, modes of transmission, symptoms, and management. Healthcare workers did not consider Female Genital Schistosomiasis in differential diagnoses of women presenting with gynecologic symptoms except sometimes in patients who did not respond to the initial therapy for sexually transmitted infections. Healthcare facilities had limited capacity to manage Female Genital Schistosomiasis. Our findings show critical gaps in both the knowledge of healthcare workers to manage Female Genital Schistosomiasis and in the capacity of healthcare facilities to manage it. To fill these gaps, two urgent needs must be fulfilled: first, training healthcare workers (particularly those working in schistosomiasis-endemic settings) on Female Genital Schistosomiasis, and second, stocking healthcare facilities with necessary medical equipment and supplies for managing this disease.