A method of configuring a time-of-flight positron emission tomography (PET) system includes determining a set of parameters of a detector of the PET system. Each parameter is configured to affect photon travel within the detector. The method further includes simulating operation of the detector to generate a photon detection timing data profile for a plurality of depth of interaction (DOI) positions within the detector via a simulation model of the detector configured in accordance with the set of parameters, and determining a time-of-flight correction factor for each DOI position of the plurality of DOI positions based on the simulated operation. The correction factor is indicative of a time offset of the photon detection timing data profile.