Individual choices shape life course trajectories of brain structure and function beyond genes and environment. We hypothesized that individual task engagement in response to a learning program results in individualized learning biographies and connectomics. Genetically identical female mice living in one large shared enclosure freely engaged in self-paced, automatically administered and monitored learning tasks. We discovered growing and increasingly stable interindividual differences in learning trajectories. Adult hippocampal neurogenesis and connectivity as assessed by a high-density multielectrode array positively correlated with the variation in exploration and learning efficiency. During some tasks, divergence transiently collapsed, highlighting the sustained significance of context for individualization. Thus, equal environments and equal genes do not result in equal learning biographies because life confronts individuals with choices that lead to divergent paths.