Background Viral respiratory infections trigger pulmonary exacerbations (PEs) in children with cystic fibrosis (CF), but their clinical impact is not well understood. Methods A retrospective review of pediatric patients with CF who underwent nasopharyngeal respiratory viral panel testing during hospitalization for a PE between 2011 and 2018 was conducted. Patients were dichotomized into viral‐positive and viral‐negative groups. The results of spirometry, respiratory cultures, duration of hospitalization, and risk for subsequent PEs were analyzed. Results Ninety‐five patients had 210 hospitalizations for PE (viral‐positive = 71/210, 34%) during the study period. Rhinovirus/enterovirus was the most common virus (52/71, 73%) identified. Viral‐positive patients were younger (p < 0.001), had higher baseline forced expiratory volume in 1 s (FEV1) (p = 0.037), continued to maintain higher FEV1 at 3 and 6 months following PE (p = 0.003 and 0.002, respectively), and had a shorter duration of hospitalization (p = 0.006) compared to the viral‐negative group. There was no difference between the two groups in the rate of recovery of FEV1 at 3 and 6 months following PE (p = 0.71 and 0.405, respectively), time to the next PE (hazard ratio = 1.34, p = 0.157), number of subsequent PEs in 6 months (p = 0.99), or Pseudomonas aeruginosa (PA) acquisition (p = 0.707). Conclusions In this single pediatric CF center cohort, one‐third of PEs requiring hospitalization were associated with a viral infection, with rhinovirus/enterovirus being the most common. Viral‐positive PEs were not associated with a greater decline or delayed recovery of lung function, increased risk for PA acquisition, shortened duration to next PE, longer hospital stay, or an increase in the frequency of subsequent PEs in 6 months compared to viral‐negative PEs.