Background: Triple therapy with cystic fibrosis transmembrane conductance regulator (CFTR) modulators in patients with cystic fibrosis (CF) has led to a shift in the nutritional management of the disease. Correct assessment of nutritional status is crucial due to its significant impact in pulmonary function and overall patient survival. This study aims to provide mid-term data on anthropometric and body composition changes in pediatric patients treated with elexacaftor–tezacaftor–ivacaftor (ETI). Methods: A prospective, longitudinal, multicenter study was conducted involving pediatric CF patients receiving ETI therapy. Anthropometric measurements and bioelectrical impedance analysis (BIA) data were collected at baseline and after 24 months of treatment. Results: A group of 66 pediatric patients, median age of 11.11 years (IQR: 8.2–12.5), was studied. The BMI z-score increased from −0.63 at baseline to −0.38 (p < 0.001) after 2 years of ETI treatment. Somatometric parameters were compared with a retrospective cohort showing no significant results. Significant changes comparing body composition were also observed over the 24 months period: fat mass (FM) increased from 6.2 kg to 7.4 kg (p < 0.001) free fat mass (FFM), increased from 28.2 kg to 34.2 kg (p < 0.001) and body cellular mass (BCM), increased from 7.8 kg to 8.7 kg (p = 0.02). Conclusions: Pediatric patients undergoing ETI treatment showed mid-term improvements in anthropometric parameters, alongside notable changes in body composition. Long-term studies are needed to confirm these findings and to better understand the implications for pediatric CF care.