Ghanaian secondary schools face challenges in addressing mental health issues among students, impacting their academic performance. A randomized controlled trial was conducted with 200 secondary schools in Nigeria, randomly assigned to either intervention (counseling programme) or control groups. Data collection included pre- and post-intervention assessments of students' academic performance. The proportion of students showing significant improvement in academic scores was found to be 35% higher in the intervention group compared to controls at the end of two years, with a confidence interval (CI) for this difference being [20%, 48%]. School-based mental health counseling significantly enhances academic performance among secondary school students in Nigeria. Further studies should explore scalability and cost-effectiveness to implement these programmes across more schools. Treatment effect was estimated with $\text{logit}(p_i)=\beta_0+\beta^\top X_i$, and uncertainty reported using confidence-interval based inference.