In the present work, forced convective heat transfer of water/functionalized multi-walled carbon nanotube (FMWCNT) nanofluid in a two-dimensional microchannel is investigated. To solve the governing Navier-Stokes equations and discritization of the solution domain, the numerical method of finite volume and SIMPLE algorithm have been employed. Walls of the microchannel are under a periodic heat flux, and slip boundary conditions along the walls have been considered. Effect of different values of shear forces, solid nanoparticles concentration, slip coefficient, and periodic heat flux on the flow and temperature fields as well as heat transfer rate has been evaluated. In this study, changes of the variables considered to be from 1 to 100 for Reynolds number, 0-25% for weight percentage of solid nanoparticles, and 0.001-0.1 for velocity slip coefficient. Results of the current work showed good agreement with the numerical and experimental studies of other researchers. Data are presented in the form of velocity and temperature profiles, streamlines, and temperature contours as well as amounts of slip velocity and Nusselt number. Results show that local Nusselt number along the length of microchannel changes in a periodic manner and increases with the increase in Reynold number. It is also noted that rise in slip coefficient and weight percentage of nanoparticles leads to increase in Nusselt number, which is greater in higher Reynolds numbers.