Nowadays, due to the increasing cost of industrial machines and also energy costs, using logical solutions to increase the useful life of production equipments are important. Misalignment and unbalancing are the most common factors that are causing energy loss and reduce the life of rotating machinery. Energy loss estimation has a vital role in selecting the best method for decreasing it. Several methods for modeling and detecting these faults have been presented up to now, but poor results are about the energy loss rate due to these faults. In the present paper, based on equations of motion for a system with misalignment and unbalance faults, a new idea is presented for energy loss calculation and the governing equations are solved numerically for this target. The amounts of energy loss, for both cases of with and without the faults and also for various speeds of shaft rotation, are computed and compared. The results of this theoretical investigation show that the rate of energy loss strongly depends on the amount of shaft misalignment, unbalance and speed of shaft rotation.