Purpose: Diagnostic errors contribute to patient safety risks, often arising from cognitive failures in clinical reasoning. Preceptorship is thought to improve residents’ clinical reasoning. The aim of this study was to evaluate the effect of a preceptorship program on clinical reasoning among pediatric residents. Methods: This randomized controlled trial was conducted from March 2025 to May 2025 at Dr. Soetomo General Academic Hospital, Surabaya, Indonesia. All pediatric residents were randomly allocated into two groups. The intervention group received a scheduled preceptorship program, while the control group continued with standard supervision. After 8 weeks, clinical reasoning skills were assessed using the Script Concordance Test (SCT). Data were analyzed using comparation test. End-of-program questionnaires were also reported. Results: Total 41 residents completed the study. Baseline characteristics did not differ between groups (p>0.05). Mean overall SCT scores ranged from 55% to 90% of the maximum possible score. Among 14 topics, hematology & oncology was the only topic that showed a significant difference in SCT scores between the intervention group (median, 14.28; interquartile range [IQR], 12.78–15.08) and the control group (median, 12.75; IQR, 11.49–13.63). Participants reported that preceptorship made learning more structured and interactive but noted barriers including busy preceptor schedules and lack of standardized teaching materials. Conclusion The preceptorship program resulted in a significant improvement in only one topic, which may reflect suboptimal implementation of the intervention. Despite this, participants reported positive perceptions, indicating good acceptability. More intensive and consistent preceptorship may be required to achieve measurable improvements in clinical reasoning.