Urban Kenyan children often face health challenges that can affect their academic performance. Previous studies have shown a correlation between improved health and better educational outcomes, but longitudinal data are scarce. A mixed-methods approach was employed, including pre- and post-intervention assessments with a sample size of 500 urban Kenyan children. Data were analysed using structural equation modelling (SEM) to assess the impact of health programmes on educational metrics. Prevalence rates of common illnesses among participants decreased by 20% over five years, correlating with an average improvement in standardised test scores by 15%. School health programmes significantly improved academic performance among urban Kenyan children over a period of five years. Continuation and expansion of these programmes are recommended to further enhance educational outcomes. Urban Kenya, School Health Programmes, Academic Performance, Structural Equation Modelling, Longitudinal Study Treatment effect was estimated with $\text{logit}(p_i)=\beta_0+\beta^\top X_i$, and uncertainty reported using confidence-interval based inference.