The effect of non-uniform heating on the heat transfer characteristics for electroosmotic flow through a microchannel has been investigated numerically. The temperature field and Nusselt number are studied by changing the normalized wavelength of non-uniform heat flux (γ) and thermal Peclet number (Pe ) in the range of 1.5 ≤ γ≤ 6 and 1 ≤ Pe ≤ 100, respectively. It is found that the intensity of maximum temperature reduces for non-uniform heating as compared to the uniform heating. The maxima of local Nusselt number increases with a decrease in the wavelength of the non-uniform heat flux. The critical Peclet number (Pec) is found such that average Nusselt number shows the monotonic and non-monotonic variation with γ.