An analysis has been made to investigate the heat transfer characteristics of electro-osmotic flow (EOF) in a non-uniform micro-channel whose walls are varying sinusoidally. The EOF is driven by the combined influence of pressure gradient and axially imposed electric field. The energy equation accounts for viscous dissipation and the Joule heating effects. The effects of slip velocity due to hydrophobic interactions at the fluid–solid interface and thermal slip (temperature jump factor) are taken into consideration. The velocity and temperature fields are obtained analytically and their numerical results have been estimated for a given set of parameters. The Nusselt number and skin-friction coefficient at the wall of the channel are furthermore derived. The results show that less pressure gradient is required to drive same amount of fluid for presence of higher electro-osmotic parameter. The velocity slip parameter has enhancing effect on axial velocity. The temperature jump factor assigned at the walls of the micro-channel has reducing effect on temperature. The study also reveals that the Joule heating parameter has controlling effect on the temperature distribution. We made a comparison for the validation of our results with the results of those available in the scientific literature and shows excellent agreement.