In this paper, we construct transient electro-osmotic flow of Burgers’ fluid with Caputo fractional derivative in a micro-channel, where the Poisson–Boltzmann equation described the potential electric field applied along the length of the microchannel. The analytical solution for the component of the velocity profile was obtained, first by applying the Laplace transform combined with the classical method of partial differential equations and, second by applying Laplace transform combined with the finite Fourier sine transform. The exact solution for the component of the temperature was obtained by applying Laplace transform and finite Fourier sine transform. Further, due to the complexity of the derived models of the governing equations for both velocity and temperature, the inverse Laplace transform was obtained with the aid of numerical inversion formula based on Stehfest's algorithms with the help of MATHCAD software. The graphical representations showing the effects of the time, retardation time, electro-kinetic width, and fractional parameters on the velocity of the fluid flow and the effects of time and fractional parameters on the temperature distribution in the micro-channel were presented and analyzed. The results show that the applied electric field, electro-osmotic force, electro-kinetic width, and relaxation time play a vital role on the velocity distribution in the micro-channel. The fractional parameters can be used to regulate both the velocity and temperature in the micro-channel. The study could be used in the design of various biomedical lab-on-chip devices, which could be useful for biomedical diagnosis and analysis.