Hair follicle transplantation is often used in the treatment of androgenetic alopecia (AGA). However, the only source of hair follicles is from human donors themselves, which limits the application of this approach. One possible solution is to reconstitute hair follicle from dissociated cells. Currently, a number of microscale technologies have been developed to create size and shape controlled microenvironments in tissue engineering. Photopolymerizable PEGDA hydrogels are often selected as promising scaffolds in engineered microtissues due to their biocompatibility and adjustable mechanical properties. Here, we fabricated an array of PEGDA microwells with center islets that mimic the architecture of human hair follicles using soft lithography. Dermal and epithelial cells were seeded in different compartments of the microstructured mould to mimic mesenchymal and epithelial compartmentalization in native hair follicles. We demonstrated that these compartmentalized microstructures support cell proliferation and cell survival over 14 days, and spreading of dermal fibroblasts was observed. This hydrogel micromould provides a potentially useful tool for engineering 3D hair follicle-mimicking complex cultures in vitro.