BACKGROUND: Defects of thymic stromal cell development may lead to congenital athymia and severe immunodeficiency. Allogeneic thymus transplantation is the only recognized effective therapy to reconstitute naïve T-cells in these rare cases, increasingly diagnosed due to worldwide newborn screening. Nevertheless, data on long-term outcomes are still missing. OBJECTIVE: Report the clinical and immunological outcomes of an adult with R255X homozygous FOXN1 mutation, followed for 19 years upon thymus transplantation with effective immune reconstitution attested by clearance of BCG dissemination and reconstitution of the naïve T-cell compartment with a full-diverse repertoire. METHODS: Longitudinal autoimmunity screening and immune profiling were complemented with T-cell studies by high-dimensional spectral flow cytometry (18 and 20 years-old) and single-cell RNA-sequencing (scRNA-seq, 18 years-old) combined with TCR and cell surface protein sequencing (CITE-seq) alongside age-matched controls. RESULTS: The uneventful clinical report contrasted with the progressive decline of circulating T-cell counts (below 400 cells/μl), with marked contraction of the naïve compartment and lack of terminal differentiation. CD4 T-cells featured a unique transcriptional signature supporting a distinct biology of T-cells developed in an allogeneic thymus implant. Regulatory T-cells presented a suppressive signature, which may explain the absence of autoimmune manifestations. The expanded oligoclonal population of double-negative αβ T-cells identified before the transplant persisted with similar phenotype with transcriptional evidence of a role for the EGFR pathway in its maintenance. CONCLUSION: This rare case supports a distinct biology of T-cells educated in allogeneic thymus, with poor naïve T-cell sustainability emphasizing the need for research on immune reconstitution mechanisms.