Most studies in children of school-age have focused on enrolled pupils because of ease of access, organization and logistics. As a result there are few reports on their non-enrolled counterparts. A randomized case-control study to assess the prevalence of helminths infection and nutritional status (anthropometry, anaemia and diet history) of non-enrolled (cases), and enrolled school-age children (controls) was conducted in irrigated farming communities in the Bongo District of Ghana. Out of the 329 children, 148 (44.98%) non-enrolled and 181 (55.02%) enrolled children were used for the studies. Enrolled children significantly benefitted from the national deworming programme (OR = 115.65, 95% CI = 22.29 – 599.95, p < 0.001). Three parasites; hookworm, Schistosomamansoni and Schistosoma. Haematobium were recorded. The prevalence of S. mansoni in non-enrolled children was 14.94% significantly higher than 5.52% in their enrolled counterparts (Ãâ Ãâº2 = 42.20, df = 19, p = 0.002). Macro-haematuria was observed in 8.8% of the non-enrolled and 1.8% enrolled children which was significantly different (Ãâ Ãâº2 = 16.48, df = 2, p = 0.000). Also, 25% of non-enrolled had trace to high micro-haematuria compared to 15.88% of their enrolled counterparts which was significantly higher (Ãâ Ãâº2 = 18.42, df = 6, p = 0.005). 36.49% of non-enrolled had proteinuria compared to 38.24% of enrolled children which was significantly lower in the former (Ãâ Ãâº2= 15.11, df = 6, p = 0. 017). 83% of the 5-8 years age group were anaemic and was significantly high compared to the other age group (OR = 5, CI 95 = 2.34 – 10.68, p = 0.000). The mean daily vitamin C intake was significantly higher in nonenrolled (102.1± 33.8) than enrolled children (76.4 ± 24.2), [p = 0.000].Policymakers and health practitioners should expand the national deworming programme to the non-enrolled children. The School feeding and nutritional supplements should also be considered.