Geckos feature a large range of eye sizes, but what drives this phenotypic diversity is currently unknown. Earlier studies point towards diel activity patterns (DAP) and locomotory mode, but phylogenetic comparative studies in support of the proposed adaptive mode of eye evolution are lacking. Here we test the hypothesis of DAP as the driver of eye size evolution with a dataset on 99 species of gecko. Results from phylogenetic generalized least square analysis (PGLS) and multivariate model-fitting reveal smaller eyes in diurnal geckos consistent with different phenotypic optima. However, Bayesian analyses of selective regime shifts demonstrate that only 2 of 9 transitions from nocturnal to diurnal activity are coupled with decreases in eye size, and 2 other regime shifts are not associated with DAP transitions. This non-uniform evolutionary response suggests that eye size is not the only functionally relevant variable. Evolutionary adaptations may therefore include different combinations of several traits (e.g., photoreceptors), all with the same functional outcome. Our results further demonstrate that DAP only partially explains eye size diversity in geckos. As open habitats favor the evolution of large eyes while obstructed habitats favor small eyes, the degree of habitat clutter emerges as another potential axis of eye diversification.