In vitro culture (IVC) of the mammalian embryo is an essential technique in reproductive technology and other related life science disciplines. Although embryos are usually cultured in groups, a single embryo culture has been highly desired for IVC to investigate developmental processes. In this study, we proposed and developed the first single embryo coculture device, which allows making an array of a single embryo coculture with endometrial cells by controlling the culture environment in a microfluidic device. To realize this concept, we investigated three key issues: selection of a culture medium for the embryo coculture with endometrial cells using a mouse embryo and endometrial cells, evaluation of an on-microporous-membrane coculture of endometrial cells and an embryo to control the polarization of endometrial cells on the membrane, and evaluation of the coculture of endometrial cells and the embryo in the microfluidic device. We successfully obtained an array of a single coculture of embryo with endometrial cells in a microfluidic device. This concept will open and enhance the management of an individual embryo for assisted reproductive technology, livestock breeding, and fundamental stage research by further development.