PurposeThe purpose of this study is to investigate heat transfer and electrokinetic non-Newtonian flow in a rectangular microchannel in the developed and transient states.Design/methodology/approachThe Carreau–Yasuda model was considered to capture the non-Newtonian behavior of the fluid. The dimensionless forms of governing equations, including the continuity equation for the Carreau–Yasuda fluid, are numerically solved by considering the volumetric force term of electric current (DC).FindingsThe impact of pertinent parameters such as electrokinetic diameter (R), Brinkman number and Peclet number is examined graphically. It is observed that for increasing R, the bulk velocity decreases. The velocity of the bulk fluid reaches from the minimum to the maximum state across the microchannel over time. At the electrokinetic diameter of 400, the maximum velocity was obtained. Temperature graphs are plotted with changes in the various Brinkman number (0.1 < r < 0.7) at different times, and local Nusselt are compared against changes in the Peclet number (0.1 < ℘e < 0.5). The results of this study show that by increasing the Brinkman number from 0.25 to 0.7, the temperature along the microchannel doubles. It was observed that increasing the Peclet number from 0.3 to 0.5 leads to 200% increment of the Nusselt number along the microchannel in some areas along the microchannel. The maximum temperature occurs at Brinkman number of 0.7 and the maximum value of the local Nusselt number is related to Peclet number 0.5. Over time in the transient mode, the Nusselt number also decreases along the microchannel. By the increasing of time, the temperature increases at given value of Brinkman, which is insignificant at Brinkman number of 0.1. The simulation results have been verified by Newtonian and non-Newtonian flows with adequate accuracy.Originality/valueThis study contributes to discovering the effects of transient flow of electroosmotic flow for non-Newtonian Carreau–Yasuda fluid and transient heat transfer through rectangular microchannel. To the authors’ knowledge, the said investigation is yet not available in existing literature.