Background: Good nutrition and physical activity of school-aged children are important for ensuring optimum growth and reducing obesity. This present study assessed associations between breakfast consumption, BMI-for-Age (BMI) and physical fitness in a cross-section of school-aged children attending government-owned primary schools in Kumasi, Ghana. Method: The sample consisted of 438 pupils (boys = 213; girls = 225; mean age 11.1 ± 1.1), attending 10 randomly selected schools. Weight (kg), height (cm) and Mid Upper Arm Circumference (MUAC) were measured for each participant, and BMI-for-age z-scores determined using the World Health Organisation (WHO) anthroplus software. Participants were stratified into thinness, normal weight, overweight/obese using WHO cut offs. Physical fitness was assessed using forward jump, left and right handgrips, flexibility, sit-ups and 50 metre run following standard procedures and converted to scores of 1 to 10 following Japanese standards, based on which percentiles were derived. Total fitness score for each pupil was computed by adding all scores. A questionnaire was used to assess meal intake patterns. Results: The mean BMI-for-age z-score for participants was − 0.24 ± 0.99. Thinness, normal weight and overweight/ obesity were 2.7, 86.5, and 10.5% respectively among the pupils. Overweight was higher in girls (14.2%) compared to boys (4.2%), p = 0.003. Similarly, mean MUAC was significantly (p = 0.021) higher in the girls (22.0 ± 3.2 cm) than the boys (20.7 ± 7.3 cm). For physical fitness, the girls scored higher in forward jump (p < 0.0001), 50-m run (p = 0.002) and overall fitness score than the boys (21.0 ± 6.2 versus 19.2 ± 8.3, p = 0.012). However, a larger proportion of boys performed excellently and poorly than girls (p = 0.019). A positive correlation was observed between BMI zscore and hand grip (r = 0.21, p < 0.001), while sit up (r = − 0.11, p = 0.018) showed a negative correlation with BMI z-score. No other fitness test varied by BMI. Overweight children performed best in handgrip. Majority of children said they engaged in exercise (89.9%) and consumed breakfast (78.9%). Breakfast consumption was not associated with BMI z-score (x 2 0.0359, p = 0.549) but non-breakfast consumers performed better in 50 m run compared to consumers (7.0 seconds ± 2.3 vrs 6.3 seconds ± 2.5, p = 0.022). Children who reported to exercise were physically fitter than those who did not.(Continued on next page)