Auger emitting radioisotopes are of great interest in targeted radiotherapy because, once internalised in the tumour cells, they can deliver dose locally to the radiation sensitive targets, while not affecting surrounding cells. Geant4 is a Monte Carlo code widely used to characterise the physics mechanism at the basis of targeted radiotherapy. In this work, we benchmarked the modelling of the emission of Auger electrons in Geant4 deriving from the decay of ¹²³ I, ¹²⁴ I, ¹²⁵ I radionuclides against existing theoretical approaches. We also compared Geant4 against reference data in the case of ¹³¹ Cs, which is of interest for brachytherapy. In the case of ¹²⁵ I and ¹³¹ Cs, the simulation results are compared to experimental measurements as well. Good agreement was found between Geant4 and the reference data. As far as we know, this is the first study aimed to benchmark against experimental measurements the emission of Auger electrons in Geant4 for radiotherapy applications.