An out-of-yoke irradiation setup using the proton beam from a cyclotron that ordinary produces radioisotopes for positron emission tomography (PET) has been developed, characterized, calibrated and validated. The current from a 20 µm thick aluminum transmission foil is readout by home-made transimpedance electronics, providing online dose information. The main monitoring variables, delivered in real-time, include beam current, integrated charge and dose rate. Hence the dose and integrated current delivered at a given instant to an experimental setup can be computercontrolled with a shutter. In this work, we report on experimental results and Geant4 simulations of a setup which exploits for the first time the 18 MeV proton beam from a PET cyclotron to irradiate a selected region of a target using the developed irradiation system. By using this system, we are able to deliver a homogeneous beam on targets with 18 mm diameter, allowing to achieve the controlled irradiation of cell cultures located in biological multi-well dishes of 16 mm diameter. We found that the magnetic field applied inside the cyclotron plays a major role for achieving the referred to homogeneity. The quasi-Gaussian curve obtained by scanning the magnet current and measuring the corresponding dose rate must be measured before any irradiation procedure, with the shutter closed. At the optimum magnet current, which corresponds to the center of the Gaussian, a homogenous dose is observed over the whole target area. Making use of a rotating disk with a slit of 0.5 mm at a radius of 150 mm, we could measure dose rates on target ranging from 500 mGy/s down to 5 mGy/s. For validating the developed irradiation setup, several Gafchromic R EBT2 films were exposed to different values of dose. The absolute dose in the irradiated films were assessed in the 2D film dosimetry system of the Department of Radiotherapy of Coimbra University Hospital Center with a precision better than 2%. In the future, we plan to irradiate small animals, cell cultures, or other materials or samples.