The present disclosure is directed to systems and methods for real-time control of a charged particle pencil beam system during therapeutic treatment of a patient. In an aspect, the present disclosure is directed to measuring an actual shape, an actual intensity distribution, and an actual location at isocenter of the charged particle pencil beam. The actual data is compared to model treatment data in real time to determine if a statistically significant variance occurs in which case the charged particle pencil beam can be stopped mid-treatment for correction and/or analysis.