BACKGROUND Urinary schistosomiasis remains one of the most prevalent neglected tropical diseases in the world today, particularly in developing countries including Nigeria. Chronic infection can affect the genitourinary system. School pupils, particularly the informal Almajiri school pupils are at increased risk of the infection. OBJECTIVE The objective of this study was to determine and compare the prevalence and intensity of urinary schistosomiasis among primary and Almajiri school pupils in Kura Local Government Area (LGA) aged 5-15 years. We also aim to determine the presence of haematuria and proteinuria among these pupils. METHODS It was a cross-sectional comparative study involving 200 primary and 200 Almajiri school pupils aged 5-15 years in Kura LGA who met the inclusion criteria. Urine samples were analysed by the dipstick urinalysis and microscopically examined for the egg S. haematobium. RESULTS The Almajiri school pupils had a significantly higher infection (55.5%) than the primary school pupils (43.0%). The infection was predominantly of light intensity in both school types (67%). The overall mean egg intensity was 51.6 ± 35 EPC. The infection was higher among boys and those aged 10 years and above. Majority of the pupils had microhaematuria (88.3%) and and proteinuria (71.1%), which were statistically significantly associated with the infection with P < 0.1 and P < 0.001, respectively. CONCLUSIONS The prevalence of urinary schistosomiasis is higher among the Almajiri school pupils compared to the primary school pupils. Control programmes should focus on these Almajiri pupils in addition to the primary school pupils.