Background: The epithelial microenvironment is involved in thymus aging, but the possible role of EphB receptors that govern the thymic epithelium development has not been investigated. Herein, we study the changes undergone by the thymus of EphB-deficient mice throughout their life. Results: Immune alterations occurring throughout life were more severe in mutant than in wild-type (WT) mice. Mutant thymuses exhibit lower cellularity than WT ones, as well as lower proportions of early thymic progenitors cells and double-positive (CD4 + CD8 +) thymocytes, but higher of double-negative (CD4 − CD8 −) and single-positive (CD4 + CD8 − , CD4 − CD8 +) cells. Throughout life, CD4 + naïve cells decreased particularly in mutant mice. In correlation, memory T cells, largely CD8 + cells, increased. Aged thymic epithelium undergoes changes including appearance of big epithelial free areas, decrease of K8 + K5 − areas, which, however, contain higher proportions of Ly51 + UEA1 − cortical epithelial cells, in correlation with reduced Aire + medullary epithelial cells. Also, aged thymuses particularly those derived from mutant mice exhibited increased collagen IV, fat-storing cells, and connective cells. Conclusions: The absence of EphB accelerates the alterations undergone throughout life by both thymic epithelium and thymocytes, and the proportions of peripheral naïve and memory T cells, all of which are hallmarks of immune aging.