Over the past two decades, there has been growing interest in analyzing the effects of educational programs on outcomes using process data from computer-based testing and learning environments. However, most analyses focus on final outcomes at the end of a test or session, overlooking their functional nature over time and neglecting causal mechanisms. To address this gap, this article proposes a novel causal mediation framework for identifying and estimating functional natural direct effects, functional natural indirect effects, and functional total effects, along with their subgroup effects. We define these effects using potential outcomes and provide nonparametric identification strategies depending on whether post-treatment covariates are present or not. We then develop estimation methods using generalized additive models, a flexible and robust tool for analyzing functional data. Through a simulation study, we assess the finite-sample performance of the proposed approach by comparing it to parametric regression methods. We also demonstrate our approach by examining the effects of extended time accommodations on two functional outcomes using process data from the National Assessment of Educational Progress. Our mediation approach with functional outcomes effectively captures dynamic causal mechanisms underlying the program’s effects and pinpoints when and for whom each effect manifests throughout the testing period.