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Educational programs for individual subjects are often administered in clustered settings, complicating the evaluation of mediational processes using conventional parametric causal mediation analysis methods based on single-level models and standard error estimation techniques. This study suggests enhancing the estimation of natural direct and indirect effects through cluster bootstrapping and fixed effects modeling, offering robustness against cluster-level confounding and variation. A real data analysis of the early Head Start program's impact on vocabulary development illustrates how different approaches to addressing clustering may lead to different conclusions. A pilot simulation demonstrates that fixed effects modeling with cluster bootstrapping yields more accurate estimates than single-level approaches. This underscores the need to address clustered data structures for valid causal mediation analysis in educational research.