Background: Congenital duodenal obstruction is the most common congenital abnormalities in newborn. Almost 50% of all cases of congential abnormalities is duodenal obstruction. Several conditions of congenital obstruction can worsen a patient's prognosis, such as prematurity, low birth weight (LBW), other congenital abnormalities, type of obstruction, and the type of surgery performed. Objective: To identify prognostic factors for mortality in patients with congenital duodenal obstruction in Dr. Moewardi Hospital Surakarta. Methods: This study was a retrospective descriptive study with cross-sectional approach. Data of congenital duodenal obstruction patients were taken from inpatient medical records from January 2019 to December 2020 at Dr. Moewardi Hospital, Surakarta. Diagnosis, gestational age, birth weight, type of obstruction, other congenital abnormalities, and surgical procedure performed were also recorded. The data were then processed using SPSS 25.0, and one-way Fisher's Exact test was performed. Results: From 20 samples of patients with congenital duodenal obstruction, most of them were born at term pregnancy were 13 patients (65%). There were 11 (55%) babies who died. Based on the type of obstruction, total obstruction type were 12 (60%) patients with mortality rate 81.8%. 13 patients (65%) had comorbid congenital abnormalities. The most commonly performed surgical procedure was duodenojejunostomy (45%). Fisher's Exact test also showed statistically significant data (P = 0.04). Conclusion: There were 20 samples with congenital duodenal obstruction. The total obstruction type had the highest mortality rate. Other variables such as gestational age, birth weight, and other congenital abnormalities did not significantly influence mortality in this study.