We investigate the effect of Joule heating on the pseudosteady-state behaviour of the isotachophoretic transport of ionic species in a 2-D microchannel with both ends kept at constant temperature. The Joule heating-induced temperature gradient may significantly alter ion transport by changing the thermophysical properties. The equations governing the phenomena are the Nernst-Planck equations for transport of ions coupled with the equation for temperature field. A finite volume based QUICK ( Quadratic Upwind Interpolation Convection Kinematics) scheme is used to compute the governing equations. The stack of ionic species in the channel occurs according to the increasing order of electrical conductivity or decreasing order of electric field. The heat generation is highest at the region filled by low conducting electrolyte (TE) and leads to a high temperature plateau. An inclination in temperature profile arises across the transition zones between two consecutive stacks of analytes. Our result shows that the ITP velocity for temperature dependent case no longer varies linearly with the applied electric field. The migration speed is greatly influenced by the ionic concentration of the sample. A parametric study is made to investigate the minimal Joule heating effect on ITP transport of analytes.