Cystic fibrosis is a progressive disease affecting various organs of the human body, including the respiratory system. While the effect of bacterial infection on cystic fibrosis outcome has been comprehensively described, little is known about the impact of viruses. We collected 49 nasopharyngeal swabs derived from cystic fibrosis paediatric patients during pulmonary exacerbation and tested them for the presence of respiratory viruses to elucidate the influence of the viral infection on their clinical outcome. We found that patients infected with a virus, compared to those in whom molecular testing for viruses was negative, are characterised by a better clinical outcome, as measured by the Shwachman–Kulczycki score (p = 0.006) and have better chest radiographs, as indicated by the Brasfield score (p = 0.002). Moreover, these patients have lower C-reactive protein levels (p = 0.002). We assume this unexpected association of better clinical outcomes during viral infection should be studied further.