Electrokinetic flow is an efficient means to manipulate liquids and samples in lab-on-a-chip devices. It has a number of significant advantages over conventional pressure-driven flow. However, there exists inevitable Joule heating in electrokinetic flow, which is known to cause temperature variations in liquids and draw disturbances to electric, flow and concentration fields via temperature-dependent material properties. Therefore, both the throughput and the resolution of analytic studies performed in microfluidic devices are affected. This article reviews the recent progress on the topic of Joule heating and its effect in electrokinetic flow, particularly the theoretical and experimental accomplishments from the aspects of fluid mechanics and heat/mass transfer. The primary focus is placed on the temperature-induced flow variations and the accompanying phenomena at the whole channel or chip level.