In this paper, we investigate the peristaltic transport of a two layered fluid model consisting of a Jeffrey fluid in the core region and a Newtonian fluid in the peripheral region. The channel is bounded by permeable heat conducting walls. The analysis is carried out in the wave reference frame under the assumptions of long wave length and low Reynolds number. The analytical expressions for stream function, temperature field, pressure-rise and the frictional force per wavelength in both the regions are obtained. The effects of the physical parameters associated with the flow and heat transfer are presented graphically and analyzed. It is noticed that the pressure rise decrease with increasing slip parameter β in the pumping region (ΔP > 0). The temperature field decreases with increasing Jeffrey number and the velocity slip parameter; whereas the temperature field increases with increasing thermal slip parameter. Furthermore, the size of the trapped bolus increases with increasing Jeffrey number and decreases with increasing slip parameter. We believe that this model can help in understanding the behavior of two immiscible physiological fluids in living objects.