Background <p>Nurses working in NICU and PICU frequently encounter ethical dilemmas that can erode their moral sensitivity and trigger distress that can jeopardize patient safety, undermine staff well-being, and hinder interprofessional collaboration. Traditional lecture-based ethics education often fails to engage nurses deeply or produce durable improvements in ethical reasoning. The flipped classroom (FC) model, which delivers core content before class and uses face-to-face time for interactive case discussions, may offer a more effective route to strengthening ethical insight and reflective practice in critical care settings.</p> Methods <p>In this randomized controlled trial, 80 NICU and PICU nurses at Afzalipour Hospital in Kerman, Iran, were enrolled by census sampling and randomly assigned (1:1) to an FC intervention group (<i>n</i> = 40) or a control group (<i>n</i> = 40). Both groups received the hospital’s standard ethics in-service program. The FC group additionally reviewed five digital pre-class modules over 20 days and attended three 2-hour interactive workshops on managing moral distress, building resilience, and heightening moral sensitivity. Outcomes were assessed at baseline, immediately post-intervention, and at two-week follow-up using Corley’s Moral Distress Scale–Revised and Lützén’s Moral Sensitivity Questionnaire. Within-group changes were evaluated with paired t-tests and between-group differences with independent t-tests (α = 0.05).</p> Results <p>Baseline demographic and professional characteristics were similar between groups (all <i>p</i> &gt; 0.05). The FC group’s mean moral distress score decreased from 70.44 ± 26.35 at baseline to 50.60 ± 36.46 immediately post-intervention (<i>p</i> &lt; 0.001) and remained significantly lower at two-week follow-up (<i>p</i> &lt; 0.01). Their mean moral sensitivity score increased from 171.37 ± 23.15 to 182.97 ± 18.24 immediately after training (<i>p</i> = 0.003) and remained elevated at follow-up (<i>p</i> = 0.005). The control group indicated no significant reduction in moral distress (<i>p</i> = 0.07) and only a non-sustained rise in moral sensitivity (<i>p</i> = 0.20).</p> Conclusions <p>Flipped classroom–based ethics education substantially mitigates moral distress and enhances moral sensitivity among NICU and PICU nurses compared with conventional training. Incorporating FC strategies into critical care nursing curricula may strengthen ethical competence in demanding clinical settings.</p> Trial registration <p>IRCT20220203053920N4 (Registered 03 February 2022).</p>