BackgroundImmunity reconstitution (IR) is crucial for pediatric patients undergoing hematopoietic stem cell transplantation (HSCT), but the impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on lymphocyte subsets post-transplant remains unclear. Therefore, we assessed immune cell dynamics in children after SARS-CoV-2 infection.MethodsWe enrolled 42 children, including 21 post-HSCT SARS-CoV-2 infected and 21 matched, non-infected historical controls (1:1 matching based on propensity scores). The time from HSCT to SARS-CoV-2 infection in the infected group was determined by the beginning of follow-up for the non-infected group. The primary endpoint was 270-day IR kinetics post-infection.ResultsOur findings showed similar recovery trends between the infected group and non-infected group both in UCB and HID recipients. In the UCB cohort, the NK cell reconstitution in the infected group was poorer compared to the non-infected group, but this difference did not reach statistical significance (P = 0.178). Furthermore, HID transplantation might be a trend towards poor CD19+ T-cell reconstitution [hazard ratio (HR): 0.43, 95% CI: 0.18–1.04, p = 0.06]. No statistically significant difference was observed in terms of secondary infections across the UCB (P = 0.150) and HID (P = 0.980) cohorts as well as there was no discernible difference in overall survival between the two groups (P = 1).ConclusionsOur analysis reveals that SARS-CoV-2 might temporarily impaired the IR process in the short term, with recovery to a comparable trend as observed in non-infected patients approximately 9 months post-infection.