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Background: This study assessed the characteristics of neonates with duodenal atresia (DA) who developed transient postoperative cholestasis which resolved spontaneously, without identifiable congenital anomalies or surgical complications, and identified potential risk factors for cholestasis. Methods: Neonates with DA who underwent surgery at our institution between January 2009 and July 2022 were retrospectively reviewed. Demographic factors, intraoperative findings, placement of a trans-anastomotic tube (TAT), and postoperative outcomes were compared between patients who developed cholestasis (conjugated hyperbilirubinemia >2.0 mg/dL) after surgery (Group A) and those who did not (Group B). This report is a retrospective cohort study and complies with the STROBE statement. Results: Among 19 neonates with DA, 6 (31.6%) developed cholestasis after surgery, with the highest direct bilirubin value being 4.3 (2.4-6.5) mg/dL (median, [range]) on postoperative day 14.5 (2-23) that persisted for 67 (47-116) days until spontaneous resolution. Neonates in Group A had a significantly younger gestational age (36.6 vs. 38.0 weeks) (median) (p=0.038), a higher rate of Down syndrome (66.7 vs. 15.4%) (p=0.046), a higher rate of TAT placement (66.7 vs. 15.4%) (p=0.046), and longer administration of total parenteral nutrition (15.5 vs. 7.0 days) (p=0.027) than those in Group B. Conclusion: Transient cholestasis after surgery for DA seemed to be associated with prematurity, Down syndrome, parenteral nutrition, and TAT placement.