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Abstract Background Schistosomiasis causes substantial chronic morbidity in sub-Saharan Africa, yet case definitions, clinical management guidance, and health worker training for schistosomiasis-related morbidity remain limited. Methodology We conducted a qualitative needs assessment for schistosomiasis morbidity management. Workshops were held over one day in each of Pakwach, Buliisa, and Mayuge Districts in Uganda in October 2024. 105 government health workers participated including clinicians, nurses, laboratory technicians, sonographers, and district health managers from health facilities at different levels of care. The workshops comprised six structured sessions: presentations on schistosomiasis burden in Uganda and the SchistoTrack cohort, a clinical case report by an expert clinician, an interactive session on patient case studies from the SchistoTrack cohort, mapping of patient pathways, anonymous participation and feedback, and demonstrations of schistosomiasis diagnosis. Workshop discussions were documented through notes taken in English and analysed using qualitative thematic analysis as per Braun and Clarke. Findings Health workers demonstrated substantial gaps in understanding schistosomiasis case definitions, particularly in distinguishing current infection from chronic morbidity and in grading disease severity. Patient pathways for schistosomiasis morbidity management were fragmented and inconsistent, with weak triage, unclear referral and feedback mechanisms, and limited follow-up across facility levels. Health facilities lacked essential capacity and resources, including routine access to praziquantel outside mass drug administration, diagnostic reagents, functional ultrasound equipment, trained sonographers, and standardized training and reference tools. Collectively, these gaps contributed to inconsistent clinical decision-making and under-recognition of severe schistosomiasis-related morbidity. Conclusions Integrating case management into routine health services through standardized case definitions, clearer patient pathways, and targeted practical training for health workers is essential to complement preventive chemotherapy and reduce preventable morbidity. The engagement framework and patient case studies used here can support needs-based assessments in other endemic settings to inform the development of context-appropriate clinical guidance and training programmes. Author summary Schistosomiasis is a disease common in sub-Saharan Africa that can cause serious, lifelong health problems, even after the infection itself has been treated. While mass drug administration programmes have reduced infections, we found that health facilities are often not equipped to recognize or manage the chronic illness that remains after mass drug administration. In this study, we worked with government health workers in three rural districts of Uganda to understand their experiences, challenges, and training needs related to schistosomiasis morbidity. Through interactive workshops, we learned that many health workers struggle to distinguish between current infection and long-term organ damage, especially liver disease. Patient care pathways were often unclear, referrals were poorly coordinated, and essential tools, such as diagnostic supplies, ultrasound access, and routine availability of treatment, were frequently missing. These gaps make it difficult to identify severe cases early and provide consistent care. We show that strengthening routine health services through clearer case definitions, better training, and more coordinated patient pathways is essential to reduce preventable suffering from schistosomiasis. Our approach offers a practical way to support health systems in other endemic settings facing similar challenges.