ABSTRACT Background Ventilator‐induced diaphragmatic dysfunction is associated with poor patient outcomes. However, the detailed pathophysiology and risk factors underlying the exacerbation of diaphragmatic dysfunction remain unclear. We aimed to evaluate the effect of sedation on diaphragmatic function in extremely preterm infants (EPIs) using ultrasound. Methods A prospective observational study was conducted on 30 EPIs requiring mechanical ventilation within 6 h of birth between July 2020 and September 2023. Diaphragm ultrasound was performed to measure the end‐expiratory and end‐inspiratory thicknesses of the diaphragm (Tde and Tdi, respectively) and to calculate diaphragm thickening fraction (DTF) after birth and on day 1 of life. Patients receiving continuous fentanyl administration on day 1 were categorized into the sedated group, whereas those not receiving were categorized into the non‐sedated group. Changes in Tde, Tdi, and DTF from day 0 to day 1 were compared between groups. Results Baseline Tde, Tdi, and DTF did not differ between groups, and both groups showed significant reductions in Tde, Tdi, and DTF from day 0 to day 1. Analysis of covariance after controlling for gestational age and birth weight revealed that sedation significantly affected the change ratios (Tde, −0.343 vs. −0.157, p = 0.038; Tdi, −0.4 vs. −0.169, p = 0.008; DTF, −0.385 vs. −0.194, p = 0.038). Conclusion In this pilot study, we found that sedation may affect Tde, Tdi, and DTF in ventilated EPIs, and that larger, adequately powered studies are required to validate these preliminary findings.