This paper presents a control system algorithm for a five-axis parallel mechanism system (PMS) CNC milling machine based on a 6-DOF Stewart platform parallel manipulator with a universal-prismatic-spherical (UPS) configuration. The control system reads the G-Code commands as standard CNC machine language, then extract data points and interpolates them to generate the robot trajectory patterns as motion references. Then, the control system uses the modified inverse kinematic equation to determine the length of each link to move the end effector to track the trajectory patterns from the previous G-code extraction process. The inverse kinematic equation is modified especially for the five-axis PMS CNC milling machine by including machine-offset and tools-offset parameters so it will be easier for the control system to implement the kinematic equation. As expected, the system simulation results successfully followed the G-Code program moving commands. The average error of the length control system is 0,1 mm, while the average error of the length change rate control system is 1,8 mm/s. The maximum error is 26.9 mm was caused by the system's inability to follow the motion profile in transient. It can be concluded that 6-DOF Stewart platform parallel structures,which provide better performance than serial structures, can be implemented as a new concept for the motion mechanism of five-axis CNC milling machines. The five-axis PMS CNC milling machine also promises better performance than conventional five-axis gantry structures CNC.