This study addresses a current research gap in Physics concerning Methodological evaluation of secondary schools systems in South Africa: difference-in-differences model for measuring yield improvement in South Africa. The objective is to formulate a rigorous model, state verifiable assumptions, and derive results with direct analytical or practical implications. A mixed-methods design was used, combining survey and interview data collected over the study period. 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 South Africa: difference-in-differences model for measuring yield improvement, South Africa, Africa, Physics, original research 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.