This paper focuses on the comparative electrokinetic micromixing of non-Newtonian fluid in cylindrical microchannels with surface potential heterogeneity due to sudden constriction/expansion. In numerical simulations, the rheology of the aqueous solution is considered to follow power-law characteristic. Based on the Poisson–Nernst–Planck model, the simulations are performed to investigate the mixing efficiency and pressure drop for constricted and expanded configurations over a wide range of the flow behavior index, potential patch strength, and geometric parameters. The results show that, irrespective of geometric configurations, the mixing efficiency can be improved significantly by increasing the flow behavior index, geometric parameters, and the overpotential patch strength. In addition, it is also revealed that the constricted geometry yields better mixing as compared to the other configuration, but the average pressure drop shows reverse characteristics. Thus, a parametric relationship is tried to be established between mixing efficiency and pressure drop for both these configurations to propose an effective and efficient micromixer, which can produce maximum possible mixing efficiency with minimum pressure drop.