Background <p>Since the lifting of COVID-19 control measures, infections by common respiratory pathogens have emerged as a public health issue, and the impacts on vulnerable children with wheezing illnesses remain uncertain.</p> Methods <p>This prospective study enrolled children (&lt; 18 years) hospitalized for wheezing disorders in Hong Kong (2016‒2025). Nasopharyngeal aspirates collected within 12 h of admission were tested via rapid antigen detection, viral culture, and multiplex polymerase chain reaction (PCR) for respiratory viruses. Bacterial pathogens were identified through cultures of blood/airway specimens or PCR, including <i>Chlamydia pneumonia</i> and <i>mycoplasma pneumoniae</i> detection via PCR.</p> Results <p>A total of 2499 children [66.8% male, median age 2.9 (3.6) years)] with 3272 admissions due to wheezing disorders were identified. There was a substantial reduction in pediatric wheezing admissions during the COVID-19 pandemic (February 2020 to January 2023) compared to the pre-pandemic period (September 2016 to January 2020). After removing pandemic restrictions, wheezing admissions drastically increased from February 2023 to February 2025, exceeding the pre-pandemic level. A fivefold increase was observed in admissions due to “bronchiolitis” compared with that during the pandemic period (<i>P</i> &lt; 0.001). The post-pandemic proportion of respiratory syncytial virus (RSV) significantly increased, especially among those under 5 years of age (<i>P</i> &lt; 0.01). Coinfections with multiple pathogens were more common during and after the pandemic than pre-pandemic (<i>P</i> &lt; 0.05).</p> Conclusions <p>Lifting restrictions led to a resurgence of wheezing admissions and respiratory infections. Continued pathogen monitoring in the post-pandemic era is crucial, and preventive measures for future health crises are needed.</p> Graphical abstract <p></p>