We investigate the flow and mixing characteristics for an electroosmotic flow through a wavy micromixer using surface charge heterogeneity. The Laplace equation for the external electric field, Poisson-Boltzmann equation for potential distribution, and continuity and momentum equations for fluid flow and species transport equation have been solved by imposing the appropriate boundary conditions using a finite element method-based numerical solver. The results are presented by varying the phase lag of sinusoidal zeta potential between the two walls (Δφ), Debye parameter (κ), geometrical wave number (n), dimensionless wall amplitude (α), and diffusive Peclet number (Pe). The results reveal that the phase lag has a strong confluence on the flow field and mixing performance together with other physicochemical parameters. The strength of primary flow as well as the size of the recirculation zones increases with Δφ and κ, and additional recirculation zones are formed in the core of the mixer for Δφ = 0. The value of mixing efficiency is close to 100% up to a critical value of Pe (PeCri), the value of which is greater for the nonuniformly charged surface potential with a nonzero phase lag. For thinner EDL (κ = 150), a fully mixed state based on 90% mixing is achieved up to higher values of Pe with a higher flow rate at Δφ = π/2 and π. Also, for Δφ = π/2, the mixing efficiency as well as the flow rate enhances with the amplitude of the channel walls for PeCri≤ Pe ≤323.5. Moreover, for Δφ = 0, the value of mixing efficiency increases with α for 786 ≤ Pe ≤1000 with a 9.17% decrement in the flow rate for the change in α from 0.05 to 0.25.