Methods are provided for calibrating an ion beam scanner in an ion implantation system, comprising measuring a plurality of initial current density values at a plurality of locations along a scan direction, where the values individually correspond to one of a plurality of initial voltage scan intervals and one of a corresponding plurality of initial scan time values, creating a system of linear equations based on the measured initial current density values and the initial voltage scan intervals, and determining a set of scan time values that correspond to a solution to the system of linear equations that reduces current density profile deviations. A calibration system is provided for calibrating an ion beam scanner in an ion implantation system, comprising a dosimetry system and a control system.