Background Good nutritional status of school-aged children is crucial in achieving improved cognition. The objective of this study was to assess the relationship between nutritional status and cognition of school-aged children in the Kumasi metropolis, Ghana. Methods 389 children were selected from ten government-owned schools. Socio-demographic and anthropometric data were collected. Blood samples were collected and analyzed for nutrients levels. Dietary intakes were assessed using food frequency questionnaire and previous day’s nutrients intake. Cognition test was performed using the Ravens Colored Progressive Matrix (RCPM). Results Mean age of participants was 8.9±1.4 years, mean RCPM score was 17.9±5.4. More girls scored RCPM below the 40th percentile (45.5%) than boys (33.7%), while mother’s level of education significantly associated with RCPM percentiles of the children (p = 0.037). Four dietary patterns were generated from food frequency data, and scores of the second pattern, depicting vegetables, non-fruits, bread and cereals, showed a weak negative correlation (r = -0.132, p = 0.026) with previous day’s dietary zinc intake. Cognitive status did not vary by anthropometric and dietary patterns. More anemic (54.4%) than non-anemic (33.3%) children were below the 40th RCPM percentile. Mean previous day’s intake for folate (p<0.001), vitamin B6 (p = 0.018), iron (p<0.001), and zinc (p = 0.001) differed significantly between the cognitive test score percentiles of the children. Spearman rank correlation showed weak positive associations between RCPM score and hemoglobin (r = 0.246, p = 0.003) and serum ferritin (r = 0.176, p = 0.036). Binary regression analysis showed anemic children (aOR = 0.4; 95%CI = 0.2–0.8, p = 0.014), compared with non-anemic had decreased odds, while boys, compared with girls had increased odds (aOR = 2.0 95%CI = 1.0–4.0, p = 0.035) for scoring above the 50th RCPM percentile. Conclusions Iron status, especially hemoglobin levels, correlated with the cognitive performance of school-aged children in the metropolis. Thus nutritional strategies aimed at reducing iron deficiency anemia are needed.