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Background: Nutrition knowledge contributes significantly to the nutritional status and habits of individuals as it influences their food consumption. And body mass index (BMI) of individuals. Recent data suggests a relationship between nutrition and physical activity knowledge, attitude, practices, and anthropometric indices of Ghanaian children. Objective: To determine the relationship between nutrition and physical activity knowledge and using BMI-for-age of school-aged children. Methods: A cross-sectional study involving 591 school-aged children (8–13 years) chosen at random from schools in Ghana's Ho Municipality. Socio-demographic information was gathered. Data on nutrition and physical activity knowledge, attitude, and practice were also collected using structured questionnaires. BMI was calculated after weight and height were measured. Results: Majority of the participants had poor knowledge on nutrition (46.6%) and physical activity (49.8%) even though more children in private schools (63.3%) had better (good and excellent) knowledge in nutrition than children from public schools (48.2%). Older children (11–13 years) had 'good' knowledge of physical activity (54.7%) as opposed to younger children. Males (59.5%) and children in private schools (66.3%) also had better overall scores in combined nutrition and physical activity knowledge than their female and public-school counterparts, respectively. Physical activity knowledge was significantly (p < 0.05) associated with the BMI-for-age categories. Nutrition knowledge (p < 0.05) and total nutrition and physical activity knowledge scores (p < 0.001) were weakly but positively associated with BMI-for-age. Conclusion: The results suggest that BMI-for-age of the participants was positively correlated to the nutrition knowledge and the total nutrition and physical activity knowledge (NutPA).