Most of the applications implemented in embedded systems use timers equipped in MCU. The purposes of timer usage of the applications lie in a wide range of areas such as implementing software timers of real-time operating systems to measuring processing time of sensors. The elapsed times measured by the applications are various in length as well as in precision ranging from several us to several hundreds of ms. The paper analyzes the timing error factors caused by un- synchronizing timer clock pulse when timers are manipulated, and proposes a method of how to synchronize timer clock pulse to reduce the timing errors. As a result of an experiment, this paper shows that an error of 230us is reduced within 10us in case of appling the proposed method to a 4096Hz timer prescaled from 32768Hz by 8.