The recruitment of mural cells is critical for stabilization of nascent vessels. Stem cells from human exfoliated deciduous teeth (SHED) are considered to have mural cell-like properties. However, the signaling mechanisms that regulate the cross-talk between endothelial cells and SHED in recruiting them as mural cells is much less well understood. Herein, using a 3D biomimetic microfluidic device, for the first time, we unraveled the role of semaphorin 4D (Sema4D)–plexin-B1 signaling in the recruitment of SHED as mural cells during angiogenic sprouting and vasculature formation by endothelial cells (ECs) in a 3D fibrin matrix. The specific compartmentalized design of the microfluidic chip facilitated recreation of the multi-step dynamic process of angiogenesis in a time and space dependent manner. Enabled by the chip design, different morphogenic steps of angiogenesis including endothelial proliferation, migration & invasion, vascular sprout formation and recruitment of mural cells as well as functional aspects including perfusion and permeability were examined under various pharmacological and genetic manipulations. The results showed that Sema4D facilitates the interaction between endothelial cells and SHED and promotes the recruitment of SHED as mural cells in vascular stabilization. Our results further demonstrated that Sema4D exerts these effects by acting on endothelial–plexin-B1 by inducing expression of platelet-derived growth factor (PDGF)-BB, which is a major mural cell recruitment factor.