Entry-level Malawian children (n = 226) aged 6-8 years from two public primary schools, one a participant in a national school feeding programme (FP), the other not, were investigated for differences in nutritional and cognitive status. Stunted growth (42%) and underweight (25%) were prevalent, with no significant differences between the schools, although the school attended was a significant predictor of mid-upper arm circumference. Previous attendance at a community-based childcare centre was significantly associated with lower body weight and height. There were no significant differences in memory, reversal learning and attention outcomes between the schools. These findings report no major significant difference in nutrition or cognitive statuses between the schools, and on this basis suggest that both schools were equally in need of FP participation. More inclusive interventions and broadening/review of FP participation criteria are recommended.