Objectives: Though the prevalence of biliary atresia (BA) in the Middle East is low, its role in causing life-threatening liver diseases is disproportionately high. This study aimed to assess the prevalence, clinical presentations, diagnosis, surgical interventions, and long-term outcomes including survival rate, and to analyze prognostic factors affecting the survival of infants with BA in Bahrain. Methods: A retrospective cohort review of cases of infants diagnosed with BA between January 1993 and December 2021 at Salmaniya Medical Complex, Bahrain, was conducted. Demographic, clinical, laboratory, imaging, and histopathological data were analyzed. Outcomes measured included 5-year native liver survival (NLS) and overall liver survival (OLS) rates. Results: Out of 27 infants diagnosed with BA, 26 were included in the study. The overall prevalence was 0.007% and was significantly higher among Bahraini (0.006%) compared to the non-Bahraini population (0.001%), p < 0.001. Most patients had clay-colored stool (19 of 22; 86.4%) and hepatomegaly (18; 81.8%). Kasai procedure was performed in 23 (88.5%) patients and primary liver transplant (LT) in three. Ten (38.5%) infants required LT after the Kasai procedure. The median age at diagnosis was 56 days with interquartile range (IQR) of 30–90, and the median age at the Kasai procedure was 61 days (IQR = 56–90). NLS and OLS rates were 53.8% and 65.4%, respectively. The overall mortality rate was 34.6%. Six of the 13 (46.2%) patients who were subjected to Kasai procedure alone died awaiting LT donors. Infants with lower birth weight and older age at diagnosis had significantly better odds of survival (p < 0.029 and p < 0.044, respectively). Conclusions: BA is uncommon among infants in Bahrain. Despite effective treatment options, late diagnosis can lead to significant morbidity and mortality. Our study found a relatively low prevalence of NLS (53.8%) and OLS (65.4%). Since the majority of the diagnosed patients had presented with clay-colored stools, implementing an infant stool card for screening may be beneficial in raising parental awareness and detecting BA early. Early detection and treatment using novel therapies are likely to improve the survival rates.