Course timetabling is a time consuming problem that arise every year in each university. This is a problem that deals with assigning a large number of courses to a limited number of rooms and timeslots while satisfying a set of predefined constraints. Most of the existing timetabling systems can only be used at the university involved in the research, as each university has its own needs and requirements that differ specifically. MyCourses software tries to make a difference by allowing each university to configure which scheduling rules to use. It provides a way to schedule courses for a whole semester rather than on weekly basis. It also gives teachers the ability to easily specify their preferences, facultymembers to enter various university data and also provides an optional way for scheduling university courses. The MyCourses’s automation solver uses Simulated Annealing as an optimization technique for solving the NP hard scheduling problem. Simulated Annealing searches for a better solution as well as it has advantage to escape from local minimum by allowing to move to worse solution in comparison with other algorithms which always seeks a better one.