Human rhinovirus (HRV) is one of the most common viral causes of respiratory tract infections worldwide. The COVID-19 pandemic and non-pharmaceutical interventions significantly altered the epidemiology of respiratory viruses. This study compared HRV genotypic diversity in Mexican children with pneumonia before and during the pandemic. A total of 1983 children with pneumonia were included: 1404 pre-pandemic (2010–2013) and 579 pandemic (2021–2023). Multiplex RT-PCR was used for HRV detection. Genotyping was conducted on 136 samples with Ct < 30 by sequencing the VP4/VP2 region. Species and genotype assignments were validated using BLAST and maximum-likelihood phylogenetic analysis (MEGA XII). HRV positivity increased from 16% (233/1404) before the pandemic to 60.4% (350/579) during the pandemic period. HRV-A and HRV-C predominated in both periods; HRV-C infection was significantly associated with severe pneumonia in the pre-pandemic period (OR 3.520; p = 0.012), but this association was not observed during the pandemic. A total of 72 genotypes were identified without a dominant type in either period. HRV circulation patterns shifted in the context of the COVID-19 pandemic, with a marked increase in prevalence. The high genotypic diversity observed across both periods underscores the importance of continuous molecular surveillance to better understand HRV circulation and its clinical relevance.