Evidence shows a link between methyl-donor nutrient intakes and a child's cognitive ability. However, this is less known among Ghanaian children who might be at higher risk of methyl-donor nutrient deficiencies. This study showed comparative analysis of methyl-donor nutrient intakes and Raven's Coloured Progressive Matrices (RCPM) test performance among 2073 Ghanaian school children aged 9-13 years across four regions of Ghana. Data for the present study were obtained from the Child Nutrition, Fitness, and Cognition project; a cross-sectional survey conducted in four regions of Ghana. Dietary methyl-donor nutrient values were based on repeated 24h recall data collected during the study periods. Cognitive tests were performed on the 2073 children using Raven's Coloured Progressive Matrices (RCPM) test. We found dietary zinc (adjusted: β=0.21, p=0.003) and methionine (adjusted: β=0.60, p=0.044) intakes to be associated with RCPM scores in the linear regression model. School children living in Northern Region (adjusted OR=0.6, p<0.001, 95% CI=0.4-0.7) and Volta Region (adjusted OR=0.7, p=0.006, 95% CI=0.5-0.9) had lower odds of scoring above the 50th percentile on the RCPM test compared with those living in Greater Accra Region. Children who consumed below the RDA for dietary folate (unadjusted OR=0.8, p=0.055, 95% CI=0.7-1.0) and zinc (unadjusted OR=0.8, p=0.049, 95%CI=0.7-1.0) had lower odds of scoring above the 50th percentile on the RCPM test compared with those who consumed above the RDA for dietary folate and zinc respectively. Children who consumed below the EAR for dietary vitamin B12 (unadjusted OR=0.7, p=0.004, 95% CI=0.6-0.9) had reduced odds of scoring above the 50th percentile on the RCPM test compared with those who consumed above the EAR for dietary vitamin B12. Higher dietary methionine intake was strongly associated with higher RCPM scores. Regional differences, and children's dietary consumption below the EAR/RDA for dietary folate, vitamin B12, and zinc were associated with poor RCPM test performance. School children's nutrient intake should be prioritized for improved cognition.