Background Rheumatic heart disease (RHD) is a major and preventable cause of cardiac mortality in Sudan, particularly in Kordofan. It can be detected early with a handheld echocardiography machine. Methods A cross-sectional study was conducted in South Kordofan State, Sudan (as part of a medical convoy organized by Khartoum Medical Students Association). A team of shortly trained medical students and newly graduated doctors conducted a handheld echocardiographic screening using a simplified protocol. All suspected cases were recorded and reviewed later by a senior pediatric cardiologist. Demographic and clinical features of screened subjects were studied. Data analysis was performed using the Statistical Package for Services and Solutions (SPSS 25). Descriptive statistics were presented as “number (%)” or “mean ± SD”. RHD prevalence was expressed as cases per 1000, and Chi-Square test/Fisher’s Exact test was used to compare RHD findings between different groups. Results The disease frequency was found to be 50 per 1000. Out of 452 screened subjects (age 10-25 years), 23 were found to have RHD with a male to female ratio of 1:1.5. Echocardiographic quality was acceptable in 93% of studies. The disease was mild in 70% and moderate or involving 2 valves in 30% of patients. Patients were contacted, advised to start penicillin prophylaxis and referred to cardiologists. Risk factors for the disease included father's occupation and village of residence. Conclusion Shortly trained junior medicals can assist in RHD echocardiographic surveillance in remote areas. South Kordofan state is highly endemic for RHD and a control program needs to be implemented. Handheld echocardiography is of value for early detection and management.