Cell migration is a fundamental biological process of key importance in health and disease. Advances in imaging techniques have paved the way to monitor cell motility. An ever-growing collection of computational tools to track cells has improved our ability to analyze moving cells. One renowned goal in the field is to provide tools that track cell movement as comprehensively and automatically as possible. However, fully automated tracking over long intervals of time is challenged by dividing cells, thus calling for a combination of automated and supervised tracking. Furthermore, after the emergence of various experimental tools to monitor cell-cycle phases, it is of relevance to integrate the monitoring of cell-cycle phases and motility. We developed CellMAPtracer, a multiplatform tracking system that achieves that goal. It can be operated as a conventional, automated tracking tool of single cells in numerous imaging applications. However, CellMAPtracer also allows adjusting tracked cells in a semiautomated supervised fashion, thereby improving the accuracy and facilitating the long-term tracking of migratory and dividing cells. CellMAPtracer is available with a user-friendly graphical interface and does not require any coding or programming skills. CellMAPtracer is compatible with two- and three-color fluorescent ubiquitination-based cell-cycle indicator (FUCCI) systems and allows the user to accurately monitor various migration parameters throughout the cell cycle, thus having great potential to facilitate new discoveries in cell biology.