The Joule heating (JH) is a ubiquitous phenomenon in electrokinetic flow due to the presence of electrical potential gradient and electrical current. JH may become pronounced for applications with high electrical potential gradients or with high ionic concentration buffer solutions. In this review, an in-depth look at the effect of JH on electrokinetic processes is provided. Theoretical modeling of EOF and electrophoresis (EP) with the presence of JH is presented and the important findings from the previous studies are examined. A numerical study of a fused-silica capillary PCR reactor powered by JH is also presented to extend the discussion of favorable usage of JH.