Differences in traditional and JIT production systems can be focused on three main areas: processes, workforce and suppliers. These differences also require a different treatment of managerial control system. Control of business and financial processes are substantially different in traditional and JIT production environment. Effectively combination and development activities in the factories and JIT to achieve the desired results involves the application of scheduling, i.e. develop a detailed production plan in operation and integrated planning and control instrument, such as the Balanced Scorecard. The paper first points out the difference of two systems and in particular explains the planning and control of business and financial processes in enterprises with JIT system.