The main aim of any software development organizations is to finish the project within acceptable or customary schedule and budget. Software schedule overrun is one of a question that needs more concentration. Schedule overrun may affect the whole project success like cost, quality and increases risks. Schedule overrun can be reason of project failure. In today’s competitive world, controlling the schedule slippage of software project development is a challenging task. Effective handling of schedule is an essential need for any software project organization. The main tasks for software development estimation are determining the effort, cost and schedule of developing the project under consideration. Underestimation of project done knowingly just to win contract results into loses and also the poor quality project. So, precise schedule prediction leads to efficient control of time and budget during software development. In this paper, we developed a new technique for the prediction of schedule overrun. This paper also presents the comparison with other algorithms of schedule estimation and Tool developed by us and at last proved that Fuzzy cognitive map based prediction tool gives more accurate results than other training algorithms.