Organoids are three-dimensional and self-organizing cell cultures of various lineages that resemble structures and functions of an organ in many ways, and they are versatile tools in disease modeling and patho-mechanistic study of human diseases affecting their tissues of origin. Biliary atresia (BA), a cholangiopathy affecting the bile ducts of the liver, is a heterogeneous and multifaceted liver disease of complex pathogenesis. Cholangiopathies refer to a category of liver diseases that affect the cholangiocytes, the epithelial cells lining the lumen of the biliary trees. Biliary organoids consist of cholangiocytes in a spherical monolayer epithelium, which favorably resembles the structures and functional properties of the bile duct cholangiocytes. Biliary tissue-derived cells, pluripotent stem cells or embryonic stem cells, and hepatic progenitor cells are capable of generating biliary organoids. In the last decade, a considerable advancement has been made in the generation of biliary organoids for modeling liver physiology and pathophysiology. Using biliary organoids, scientists have advanced our knowledge underlying the pathogenic roles of genetic susceptibility, dysregulated hepatobiliary development/structure, environmental factors, and dysregulated immune–inflammatory responses to an injury in BA. This review will summarize and discuss the derivation and the use of biliary organoids in the disease modeling and patho-mechanistic study of BA.