BackgroundChildhood malnutrition still remains a major public health problem impacting negatively on the academic aptitude of school-aged children (SAC) particularly in limited resource countries. The Government of Ghana in collaboration with the Dutch Government introduced the school feeding programme (SFP) to boost the nutritional status of SAC in the country. This study sought to compare the nutritional status of SAC enrolled in schools with the SFP and SAC enrolled in schools without the SFP in place for the purpose of identifying which group has the higher rate of malnutrition.MethodsA multi-stage sampling was used to select 359 SAC between 5 and 12 years who are enrolled in primary one to six. Twelve public schools were selected, of which 6 schools benefit from the SFP and the other six do not. Anthropometric measurements were conducted for the subjects and SPSS version 20.0 was used for data entry and analysis. Chi square test was carried out to determine the difference between the two groups of schools.ResultsOf the total of 359 subjects, 55.1% were from schools that do not implement the SFP and 44.9% were from schools that implement the SFP. The prevalence of stunting among children in schools on the SFP was 16.2% compared with 17.2% among children in schools that do not implement the SFP. The prevalence of thinness was two times higher (9.3%) among children in schools on the SFP than in children in schools that do not implement the SFP (4.6%) (p = 0.028). The prevalence of overweight among children in schools on the SFP was 1.9% and 0.0% for children in schools that do not implement the SFP. Sub district, sex, age of pupil, area of residence and community type were significantly associated with stunting (p = 0.002), (p = 0.008), (p = 0.008), (p < 0.001) and (p = 0.007) respectively.ConclusionOverweight and thinness were higher among children in schools on SFP than in children in schools without SFP. An evaluation of the implementation of the school feeding programme is recommended for future studies.