Femtosecond (fs) laser ablation of metals is gaining popularity in surface texturing and micro-machining applications owing to its high precision and negligible heat affected zone. However, the wide variety of phenomena influencing the ablation, as well as the non-linear nature of the process, makes process prediction a difficult task. Femtosecond laser ablation can be represented by the two-temperature model, where, due to the very short pulse duration (shorter than the electron-phonon relaxation time), a difference between the temperature of the electrons excited by the laser pulse and the temperature of the lattice is assumed. In this work, an analytical model based on this two-temperature model is developed and validated for percussion drilling with a circularly polarized beam in a low corrosion tool steel. First, a convergence analysis is performed to determine the optimal mesh resolution for the simulation. Then, using material parameters found in the literature for stainless steel, the model is validated against percussion drilling experiments with varying number of pulses, laser fluence and pulse repetition rate. Micro-computer tomography was used for the experimental analysis of the ablated geometries. The results show a good overall agreement between the simulation and the experimental data, especially for crater depths larger than 130 μm, for which the average deviation on the depth is 6%. The model developed in this work can be used to predict the outcome of the fs laser percussion drilling process and thus to reduce the experimental costs linked to the research of the optimal process parameters. © 2022, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.