Fabrication of engineered intestinal tissues with the structures and functions as humans is crucial and promising as the tools for developing drugs and functional foods. The aim of this study is to fabricate an engineered intestinal tissue from Caco-2 cells by air-liquid interface culture using a paper-based dual-layer scaffold and analyze its structure and functions. Just by simply placing on a folded paper soaked in the medium, the electrospun gelatin microfiber mesh as the upper cell adhesion layer of the dual-layer scaffold was exposed to the air, while the lower paper layer worked to preserve and supply the cell culture medium to achieve stable culture over several weeks. Unlike the flat tissue produced using the conventional commercial cultureware, Transwell, the engineered intestinal tissue fabricated in this study formed three-dimensional villous architectures. Microvilli and tight junction structures characteristic of epithelial tissue were also formed at the apical side. Furthermore, compared to the tissue prepared by Transwell, mucus production was significantly larger, and the enzymatic activities of drug metabolism and digestion were almost equivalent. In conclusion, the air-liquid interface culture using the paper-based dual-layer scaffold developed in this study was simple but effective in fabricating the engineered intestinal tissue with superior structures and functions.