In the context of hadrontherapy, whilst ions are capable of effectively destroying radio resistant, deep seated tumors, their treatment localization must be well assessed to ensure the sparing of surrounding healthy tissue and treatment effectiveness. Thus, range verification techniques, such as online positron-emission-tomography (PET) imaging, hold great potential in clinical practice, providing information on the in vivo beam range and consequent tumor targeting. Furthermore, emitting radioactive ions can be an asset in online PET imaging, depending on their half-life, compared to their stable counterparts. It is expected that using these radioactive ions the signal obtained by a PET apparatus during beam delivery will be greatly increased, and exhibit a better correlation to the Bragg Peak. To this end, FLUKA Monte Carlo particle transport and interaction code was used to evaluate, in terms of annihilation events at rest and dose, the figure of merit in using emitter, radioactive ion beams (RI). For this purpose, the simulation results were compared with experimental data obtained with an openPET prototype in various online PET acquisitions at the Heavy Ion Medical Accelerator in Chiba (HIMAC), in collaboration with colleagues from the National Institute of Radiological Sciences’ (NIRS) Imaging Physics Team. The dosimetry performance evaluation with FLUKA benefits from its recent developments in fragmentation production models. The present work estimated that irradiations with RI, produced via projectile fragmentation and their signal acquisition with state-of-the-art PET scanner, lead to nearly a factor of two more accurate definition of the signals’ peak position. In addition to its more advantageous distribution shape, it was observed at least an order magnitude higher signal acquired from 11C and 15O irradiations, with respect to their stable counterparts.