Studying the effects of various parameters on the behavior of velocity, temperature and thus the entropy generation rate in the micro-fluidic systems to reduce loss power is very important. Minimization of entropy generation in the flow system enables us for the parametric optimization of the MHD micropumps operation. In the present study, a transient, laminar and fully developed electrically conductive fluid flow in MHD micropumps has been investigated and the temperature distribution and effects of dimensionless influencing parameters on the entropy generation rate has been presented. Pumping operator in MHD micropumps are the Lorentz forces, which is produced as a result of the interaction between magnetic and electric fields. Governing equations have been solved numerically using finite-difference (ADI) method. The results of simulation have shown good agreement with analytical results by ei-genfunction expansion method. In addition, the results are compared with experimental data from literature which confirms the accuracy of the model. The obtained results showed that aspect ratio, Hartman, Prandtl, Eckert numbers and Joule heating parameter have significant influences on the flow and temperature distribution as well as entropy generation rate in MHD micropumps that controlling them can lead us for optimized operation of MHD micropumps.