The peristaltic flow with applications of electro-osmotic phenomenon finds novel applications in microfluidic devices, biotechnology, environmental engineering, micro-reactor, and various medical devices. Owing to such motivations in mind, the objective of this analysis is to present the applications of electro-osmotic phenomenon in transport of Prandtl hybrid nanofluid due to non-uniform duct. The characteristics of hybrid nanofluid have been justified by using the single-walled carbon nanotubes (SWCNT) as well as multiple-walled carbon nanotubes (MWCNT) uniformly decomposed to engine oil base liquid. The novel aspects of viscous dissipation and Joule heating effects are attributed. The thermal problem is further influenced by electro-osmotic force. The electric field effects are attributed with the help of Poisson–Boltzmann and Nernst–Planck expressions. The simplification of electric field expressions is done via Debye–Heckle linearization. The problem is modeled under certain constraints of creeping transport and lubrication theory. The novel numerical treatment is performed with the help of Keller Box method. Physical visualization of results is performed for assisting as well as opposing electro-kinetic pumping constraints. It is claimed that the velocity profile increases in the central line of duct with variation of electro-osmotic coefficient. The heat transfer reduces due to potential ratio parameter electro-osmotic constant. Furthermore, the enhancement of Prandtl fluid parameter leads to decrement of axial pressure.