This paper presents a model specification for group comparisons regarding a functional trend over time within a trial and learning across a series of trials in intensive binary longitudinal eye-tracking data. The functional trend and learning effects are modeled using by-variable smooth functions. This model specification is formulated as a generalized additive mixed model, which allowed for the use of the freely available mgcv package (Wood in Package ‘mgcv.’ https://cran.r-project.org/web/packages/mgcv/mgcv.pdf, 2023) in R. The model specification was applied to intensive binary longitudinal eye-tracking data, where the questions of interest concern differences between individuals with and without brain injury in their real-time language comprehension and how this affects their learning over time. The results of the simulation study show that the model parameters are recovered well and the by-variable smooth functions are adequately predicted in the same condition as those found in the application.