A mathematical model is presented to study the combined viscous electro-osmotic (EO) flow and heat transfer in a finite length microchannel with peristaltic wavy walls in the presence of Joule heating. The unsteady two-dimensional conservation equations for mass, momentum, and energy conservation with viscous dissipation, heat absorption, and electrokinetic body force, are formulated in a Cartesian co-ordinate system. Both single and train wave propagations are considered. The electrical field terms are rendered into electrical potential terms via the Poisson–Boltzmann equation, Debye length approximation, and ionic Nernst Planck equation. A parametric study is conducted to evaluate the impact of isothermal Joule heating and electro-osmotic velocity on axial velocity, temperature distribution, pressure difference, volumetric flow rate, skin friction, Nusselt number, and streamline distributions.