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Malnutrition is associated with reduced learning aptitude and growth during childhood. We examined the impact of providing two school lunch variants, a standard school meal (school feeding, n = 70), or the standard meal with additional micronutrients (school feeding + micronutrient powder (MNP), n = 70), in children attending two schools in northwest Pakistan. A third local government school, where no lunch was provided (no school feeding, n = 70), served as the control. The primary outcome, cognitive function, was assessed using the Raven’s Coloured Progressive Matrices (RCPM) test, alongside haemoglobin, at three-time points: T1 (baseline, before the initiation of the school lunch programme), T2 and T3 (5 and 12 months, respectively, after the introduction of the school lunch). Data were analysed using linear mixed-effects models to contrast between trial groups, the changes from T1 to T2 and T3. Adjusted for T1 and other co-variates, improvements in the RCPM scores were significantly greater in the school feeding group at T2 (b = 1.61, (95% CI = 0.71–2.52), t = 3.52, p = 0.001) and T3 (b = 1.28, (95% CI = 0.22–2.35), t = 2.38, p = 0.019) compared with no school feeding. In addition, at T2 (b = 1.63, (95% CI = −0.10–3.37), t = 1.86, p = 0.065), there were no significant differences between school feeding + MNP and no school feeding groups. However, improvements in the RCPM scores were significantly greater in the school feeding + MNP group at T3 (b = 2.35, (95% CI = 0.51–4.20), t = 2.53, p = 0.013) compared with no school feeding. The findings indicate an improvement in cognitive performance in children who received a school …