In this paper, we formulate a mixed integer linear program (MILP) for the simulated maximum likelihood estimation (MLSE) problem and devise a Benders decomposition approach to speed up the solution process. This framework can be applied to any advanced discrete choice model and exploits total unimodularity to keep the master problem linear in the decomposition. The proposed decomposition approach is benchmarked against the original MILP formulation and PandasBiogeme. Computational experiments are performed on a binary logit mode choice model with up to 200 respondents. Results show that the Benders decomposition approach solves instances on average 35 and up to 100 times faster than the MILP while maintaining high quality solutions.