Systems and methods are provided for generating a constraint-based, time-optimal motion profile for controlling the trajectory of a point-to-point move in a motion control system. A profile generator can calculate an ST-curve motion profile that includes a jerk reference that varies continuously over time for at least one of the motion profile segments, thereby producing a smooth, time-optimal trajectory. The profile generator can create the motion profile to conform to a set of motion constraints provided by the user. The profile generator also supports calculation of time-optimal motion profiles having segments that align to the sample time of the motion control system. In some embodiments, the profile generator can efficiently generate the motion profile by performing reference calculations only for those segments that will be used in the final motion profile for a given point-to-point move.