Summary This paper presents a theoretical investigation into chaotic mixing in low Reynolds number electro-osmotic flows. In this mixing system, the primary flow is the pluglike electro-osmotic flow contributed by the permanent surface charge at the wall, and the secondary electro-osmotic flows (or electro-osmotic recirculating rolls) contributed by the field-effect-induced surface charge act as the perturbed flow. By time-periodic switching two different secondary electro-osmotic flows, it makes streamlines to cross at successive intervals and results in chaotic mixing. Dynamic system techniques such as Poincaré map and finite-time Lyapunov exponent analyses are employed to describe the behaviors of particle motion in this mixing system. Finally, the optimum operating condition (e.g. amplitude and time-switching period) for the mixing is identified