Micronutrient deficiencies and suboptimal energy intake are widespread in rural Kenya, with detrimental effects on child growth and development. Sporadic school feeding programmes rarely include animal source foods (ASF). In the present study, a cluster-randomised feeding trial was undertaken to determine the impact of snacks containing ASF on district-wide, end-term standardised school test scores and nutrient intake. A total of twelve primary schools were randomly assigned to one of three isoenergetic feeding groups (a local plant-based stew (githeri) with meat, githeri plus whole milk or githeri with added oil) or a control group receiving no intervention feeding. After the initial term that served as baseline, children were fed at school for five consecutive terms over two school years from 1999 to 2001. Longitudinal analysis was used controlling for average energy intake, school attendance, and baseline socio-economic status, age, sex and maternal literacy. Children in the Meat group showed significantly greater improvements in test scores than those in all the other groups, and the Milk group showed significantly greater improvements in test scores than the Plain Githeri (githeri+oil) and Control groups. Compared with the Control group, the Meat group showed significant improvements in test scores in Arithmetic, English, Kiembu, Kiswahili and Geography. The Milk group showed significant improvements compared with the Control group in test scores in English, Kiswahili, Geography and Science. Folate, Fe, available Fe, energy per body weight, vitamin B12, Zn and riboflavin intake were significant contributors to the change in test scores. The greater improvements in test scores of children receiving ASF indicate improved academic performance, which can result in greater academic achievement.