The contribution of age‐related structural brain changes to the well‐established link between aging and cognitive decline is not fully defined. While both age‐related regional brain atrophy and cognitive decline have been extensively studied, the specific mediating role of age‐related regional brain atrophy on cognitive functions is unclear. This study introduces an open‐source software tool with a graphical user interface that streamlines advanced whole‐brain mediation analyses, enabling researchers to systematically explore how the brain acts as a mediator in relationships between various behavioral and health outcomes. The tool is showcased by investigating regional brain volume as a mediator to determine the contribution of age‐related brain volume loss toward cognition in healthy aging. We analyzed regional brain volumes and cognitive testing data (Montreal Cognitive Assessment [MoCA]) from a cohort of 131 neurologically healthy adult participants (mean age 50 ± 20.8 years, range 20–79, 73% females) drawn from the Aging Brain Cohort Study at the University of South Carolina. Using our open‐source tool developed for evaluating brain‐behavior associations across the brain and optimized for exploring mediation effects, we conducted a series of mediation analyses using participant age as the predictor variable, total MoCA and MoCA subtest scores as the outcome variables, and regional brain volume as potential mediators. Age‐related atrophy within specific anatomical networks was found to mediate the relationship between age and cognition across multiple cognitive domains. Specifically, atrophy in bilateral frontal, parietal, and occipital areas, along with widespread subcortical regions mediated the effect of age on total MoCA scores. Various MoCA subscores were influenced by age through atrophy in distinct brain regions. These involved prefrontal regions, sensorimotor cortex, and parieto‐occipital areas for executive function subscores, prefrontal and temporo‐occipital regions, along with the caudate nucleus for attention and concentration subscores, frontal and parieto‐occipital areas, alongside connecting subcortical areas such as the optic tract for visuospatial subscores and frontoparietal areas for language subscores. Brain‐based mediation analysis offers a causal framework for evaluating the mediating role of brain structure on the relationship between age and cognition and provides a more nuanced understanding of cognitive aging than previously possible. By validating the applicability and effectiveness of this approach and making it openly available to the scientific community, we facilitate the exploration of causal mechanisms between variables mediated by the brain.