During the COVID-19 pandemic a rare new paediatric inflammatory condition (paediatric inflammatory multisystem temporally associated with COVID-19 (PIMS-TS)/MIS-C) was identified which correlated with previous or recent SARS-CoV-2 infection. PIMS-TS led to severe multi-organ inflammation, suggestive of disruption of central tolerance and thymus function. Here we investigated the possible role of the thymus in paediatric PIMS-TS. We confirmed that human thymus explants can be infected with SARS-CoV-2 in vitro. Comparison of T-cell populations in blood from PIMS-TS patients and age-matched healthy control children showed that although the overall proportions of CD4 and CD8 T-cell populations were decreased in PIMS-TS patients, the proportion of naïve cells in the CD4 population was higher in the PIMS-TS group. In PIMS-TS patients, the number of TREC in PBMC correlated strongly with the proportion of naive CD4 and CD8 T-cells, whereas this correlation was not present in healthy children. Sequencing rearranged TCRbeta and TCRalpha transcripts from FACS- sorted CD4+CD8-CD3+ and CD4-CD8+CD3+ from blood from PIMS-TS, healthy children, and additionally paediatric severe COVID-19 patients, showed that while all three groups showed similar diversity and distribution, the repertoire of the PIMS-TS and COVID-19 groups had distinctive patterns of TCR gene segment usage and VJ combinatorial usage compared to healthy controls (TRBV11-2xTRBJ2-7, TRBV11-2xTRBJ1-1, TRBV11-2xTRBJ2-5, TRBV11- 2xTRBJ2-1; TRBV29-1xTRBJ2-7, TRBV29-1xTRBJ1-1 enriched in PIMS-TS; TRBV7-9xTRBJ1-2, TRAV9-2xTRAJ30 and TRAV26-1xTRAJ39 enriched in COVID-19). The non-productive TCR rearrangements in the PIMS-TS group were also enriched for TRBV11-2, and showed bias towards distal (5’TRAV to 3’TRAJ) TCRalpha gene segment usage, suggesting involvement of the thymus in PIMS-TS.