Background: Staphylococcus aureus (S. aureus) may be related to more rapid progression of cystic fibrosis (CF) lung disease. Methods: In the AREST CF cohort study, children diagnosed with CF undergo annual bronchoscopies with bronchoalveolar lavage and ultra-low-dose, chest computed tomography (CT) up to 6-years-old. Spirometry was assessed 3-monthly from the age of 4 years. Associations between de novo S. aureus acquisition before school age and CT and lung function at ages 5–7 years were investigated. Models were adjusted for multiple markers of disease severity at baseline. Results: De novo S. aureus acquisition at 3-years-old (n/N = 12/122) was associated with increased bronchiectasis score at age 5–6 years. This association decreased but remained significant after adjustment for confounders. S. aureus at 3 was associated with significantly reduced FEF25–75 at age 5–7 years, but not with FEV1-%-predicted. Conclusion: De novo S. aureus acquisition at age 3 is associated with later bronchiectasis and FEF25–75 in children with CF.