Abstract Neonates often generate incomplete immunity against intracellular pathogens. As CD8+ T cells are essential in clearing intracellular infections, it is crucial to understand how neonatal CD8+ T cells respond to infection. We showed that neonatal CD8+ T cells fail to form memory. However, the underlying basis for this is unclear. Here, we investigated whether neonatal CD8+ T cells fail to form memory cells because (i) they have undergone more extensive homeostatic proliferation (HP) prior to infection (proliferation model) or (ii) they are created from a distinct hematopoietic stem cell (HSC) population (origin model). We first compared the behavior and gene expression profiles of different aged CD8+ T cells that had undergone similar amounts of HP. Interestingly, neonatal CD8+ T cells still possessed unique gene expression profiles and failed to form memory post-infection. Hence, the proliferation model cannot fully explain the differences. We tested the origin model by comparing neonatal and adult CD8+ T cells at the same stage of thymic development. Again, we observed distinct gene expression profiles, indicating that CD8+ T cells are created differently in neonates. To examine whether different HSCs underlie these differences, we adoptively transferred fetal and adult progenitors into adult thymii and found that fetal progenitor derived CD8+ T cells exhibited a memory phenotype and selectively formed short-lived effectors after infection. The adult progenitor derived cells exhibited a more naïve phenotype and preferentially formed memory precursors after infection. Collectively, our data extends the layered immune hypothesis to CD8+ T cells and suggests that neonatal and adult CD8+ T cells are derived from different HSCs.