Sub-millimetre precision is a crucial criterion for beam delivery in Pencil Beam Scanning (PBS) proton therapy. Nowadays, most of the therapy systems use PBS technique where single beams with a regulated number of protons are delivered sequentially to different locations within the target. Beam energy defines the depth of the beam in the target and scanner magnets deflect the beam to the desired lateral position.The PSI Gantry 2 was among the first gantries to use the PBS technique. Available clinical proton beam energies ranging from 70 MeV to 230 MeV are achieved by de-grading a 250 MeV beam, initially provided by a super-conducting cyclotron. Beam scanning is performed just before the last bending magnet producing a nearly parallel beam at iso-centre with a well-focused beam over the full scan area of 20×12 cm2. We developed a calibration algorithm for the scanner magnets in order to achieve the desirable precision of the beam in the target. Measuring the beam position with a strip ion chamber in the gantry nozzle, we parametrized the propagation of the beam to the target calculating the beam angle at different scan positions as well as all gantry angles. During 10 years of operation we performed regular Quality Assurance (QA) tests to validate parameters obtained during the system commissioning. The QA data proved a stable system operation and no parametrization update was required so far. In this contribution, we describe the calibration pro-cess of scanning magnets with respect to beam position at the isocentre and show the stability of this implementation over the time.