Purpose:To develop a mathematical model of the fluence distribution of a proton pencil beam that is partially blocked by a collimator.Methods:In one dimension, an exact analytical solution of the proton distribution behind a collimator edge was derived, taking the beam's phase space, the edge position, and the scattering downstream of the collimator as input. Extension to two dimensions was achieved using a Clarkson‐likeMethod:determine the radial distances from each calculation point to the collimator outline, calculate the beam's phase space in the direction of each radial line, apply the one‐dimensional model along each radial line, and sum the contributions. A Matlab implementation of the full model produced high‐resolution distributions with relatively short calculation times (of about 2 ms per calculation point). The model was validated by comparison to Monte Carlo simulations for select pencil beam phase space distributions and collimator shapes.Results:Agreement between model and simulation confirm the exact mathematical solution of the one‐dimensional model. In two dimensions the agreement is reasonable, but not exact, due to the approximations introduced in the Clarkson‐like method.Conclusion:A model has been developed and validated that gives the lateral fluence distribution of a pencil beam beyond a collimator. Notably, this model does not include free parameters and the final fluence is completely determined by the phase space parameters of the beam, already existing in the treatment planning system, as well as both axial and lateral position of the aperture edge. As such, it can be incorporated in a full pencil‐beam dose calculation algorithm allowing for the modeling of field‐specific collimators in proton pencil beam scanning and, potentially, the optimization of collimator shape and/or pencil phase space in addition to the customary spot weight optimization.