Abstract Patients with combined immunodeficiencies can be cured by intravenous transfer of allogeneic hematopoietic stem and progenitor cells (HSPC). However, complications such as an impaired and delayed T cell differentiation are unfortunately common, notably due to the defective thymic architecture in these patients and the requirement of HSPC homing to the thymus. To circumvent these problems, we have developed an innovative approach based on the direct targeting of HSPC into the thymus by intrathymic (IT) injection. Using ZAP70-deficient mice as a paradigm, we previously showed that IT injection of HSPC can support a long-term thymus-autonomous differentiation. Here, we show that the IT injection of WT HSPC results in a rapid engraftment and differentiation. Donor-derived thymocytes expand >100-fold, accounting for >13% of thymus cellularity by 3 weeks post IT transfer and importantly, engraftment occurs in the absence of cytoreductive conditioning. While mature CD4 thymocyte differentiation occurs in 3 weeks, the differentiation of mature Treg thymocytes requires 4 weeks. The kinetics of thymic Treg development parallels the generation of a thymic medulla, with the appearance of mature medullary thymic epithelial cells at 3–4 weeks post transplantation. Notably, the generation of the thymic medulla is associated with the differentiation of donor-derived RORγT+ innate lymphoid cells (ILC). While ILC are not required for physiological thymopoiesis, we find that they are critical for T cell differentiation in ZAP70-deficient mice presenting with an absence of the thymic medulla. These results may open new therapeutic avenues, promoting the differentiation of ILC via IT-mediated HSPC transfer, enhancing T cell differentiation. Supported by grants from ANR (CHIC) and AFM-Telethon