JAXA operates scientific balloon campaigns, aiming at obtaining scientific results through safe and reliable balloon flights. The development of the prototype of the flight prediction and control system began more than 20 years ago. It has become a mature system through many years of operation and functional enhancement and modification. The main functions of the system are implemented by a database system, which has been used for at least 82 heavy balloon experiments and 102 light balloon experiments since 2007. The applications used in client computers include more than 180 graphical user interface panels. The system is designed to incorporate redundancy for availability during balloon flight operations. Although various constraints face balloon flights, such as scientific requirements, flight safety, and severe high-altitude wind conditions, the flight prediction and control system enable us to construct a detailed flight plan and to control the flight based on predictions. In addition to the report of the system, flight prediction is explained with an example of boomerang flight control planning.