Flow-gated capillary electrophoresis (CE) is a hybrid of conventional and microchip CE since it employs a fused silica capillary as the separation channel while taking advantage of the rapid flow-gated injection that is mainly used in microchip CE. Compared with conventional CE, flow-gated CE has excellent flexibility to be combined with online sample pre-treatment procedures such as microdialysis, analyte derivatization, sample cleanup and enrichment via solid phase extraction, as well as 2D separation coupled with HPLC or CE. Additionally, the rapid sample injection may improve the separation efficiency and analytical throughput. Compared with electrophoresis on a microchip, flow-gated CE has advantages such as high separation efficiency, low capillary cost, convenient coupling with different detectors, and using fresh separation buffer. To build flow-gated CE systems, several configurations of flow-gating interfaces have been developed, out of which the transverse flow-gating configuration predominates with advantages such as small void volumes and easy preparation. Flow-gated CE has shown cutting-edge applications in in vivo measurements of neurotransmitters and in vitro monitoring of chemicals released by cultured cells or tissues. In addition, flow-gated CE, as the second dimensional separation method, has been successfully coupled with HPLC and CE to perform 2D separation. This review covers the basic instrumental setup and characteristics of flow-gated CE, flow-gating interfaces, and major applications, as well as coupling with various analytical techniques. Finally, a brief statement about the future direction of flow-gated CE is discussed. The review aims to provide the scientific community with meaningful knowledge and progress about flow-gated CE thus promoting its further development and applications.