Background COVID-19 related public health and social measures (PHSMs) worldwide have influenced respiratory virus epidemiology. In Hong Kong, paediatric hospitalisations associated with non-COVID-19 respiratory viruses declined in 2020. As PHSMs eased, rhinoviruses/enteroviruses became the primary detected respiratory viruses. This study examines the genetic diversity in resurgent human rhinovirus (HRV) cases. Methods We sequenced rhinovirus/enterovirus samples from children at Queen Mary Hospital, Hong Kong, between August 2020 and October 2021 to estimate changes in HRV genotypes and describe their epidemic characteristics. Whole genome sequencing was performed on the three most prevalent HRV genotypes to infer patterns of virus introduction and persistence. Results Despite reduced respiratory virus circulation, HRV type A and C infections persisted in children, with sporadic detection of HRV B and other respiratory viruses. A resurgence of HRV A cases in November 2020, dominated by genotypes A47 and A101, was observed during the relaxation of PHSMs between the third and fourth waves of COVID-19. Strict PHSMs implemented during the fourth wave, including school closures, substantially reduced respiratory virus circulation, though overall diversity increased due to heightened vigilance. HRV genotype A49 became predominant in May 2021 upon relaxation of control measures, with phylogenetic analysis suggesting persistence of multiple transmission lineages despite strict PHSMs. Genotypes A49 and A47 were frequently associated with upper respiratory tract infections, highlighting their epidemic potential. Conclusion This study underscores the impact of control measures on HRV genetic diversity and highlights the need for continuous surveillance and sequencing to inform public health interventions.