The embodiments of the present disclosure relate to a method and system for controlling the extraction of ion beam pulses produced by a synchrocyclotron. The synchrocyclotron comprises electrodes configured to be placed in a magnetic field. An alternating voltage is applied between the electrodes, and the frequency of the alternating voltage is modulated in a cyclic manner. In other embodiments, the method further comprises the steps of starting an acceleration cycle of the synchrocyclotron, generating a reference signal when the modulated frequency reaches a predefined value, communicating the time, at which the reference signal is generated, to the beam control elements, assessing one or more status parameters of the one or more beam control elements, and cancelling or proceeding with the extraction of the beam pulse depending on the results of the assessment.
