High-dose ibuprofen (IBU) may slow the decline of lung function in patients with cystic fibrosis (CF), but its use has been limited due to concerns over renal and gastrointestinal toxicity. In this pilot study, we examined the association of IBU with markers of acute kidney injury (AKI) in patients with CF. The effect of aminoglycoside (AG) exposure on AKI biomarkers was also examined. The AKI markers, kidney injury molecule-1 (KIM), N-acetyl-β-glucosaminidase (NAG) and urine protein, normalized for creatinine, were chosen as they are more sensitive indicators of kidney injury than changes in serum creatinine. Urine samples from 52 patients, 26 from patients who were treated with IBU, were analyzed. There was no significant association between IBU treatment and KIM-1, NAG or protein levels, compared to patients never treated with IBU. While there was an association between AG courses and KIM-1 levels, there were no differences in biomarker levels between IBU and non-IBU groups with respect to AG courses. These preliminary results suggest that IBU treatment in patients with CF may be safe with respect to renal toxicity.