This study addresses a current research gap in Agriculture concerning Methodological evaluation of secondary schools systems in Ghana: multilevel regression analysis for measuring cost-effectiveness in Ghana. The objective is to formulate a rigorous model, state verifiable assumptions, and derive results with direct analytical or practical implications. A structured analytical approach was used, integrating formal modelling with domain evidence. The results establish bounded error under perturbation, a convergent estimation process under stated assumptions, and a stable link between the proposed metric and observed outcomes. The findings provide a reproducible analytical basis for subsequent theoretical and applied extensions. Stakeholders should prioritise inclusive, locally grounded strategies and improve data transparency. Methodological evaluation of secondary schools systems in Ghana: multilevel regression analysis for measuring cost-effectiveness, Ghana, Africa, Agriculture, data descriptor This work contributes a formal specification, transparent assumptions, and mathematically interpretable claims. The empirical specification follows $Y=\beta_0+\beta^\top X+\varepsilon$, and inference is reported with uncertainty-aware statistical criteria.