Multimodal mobility systems provide seamless travel by integrating different types of transportation modes. Most existing studies model service operations and travelers’ choices independently or limited in multimodal travel options. We propose a choice-based optimization model for optimal operations of multimodal mobility systems with embedded travelers’ choices using a multinomial logit (MNL) model. We derive a mixed-integer linear formulation for the problem by linearizing transformed MNL constraints with bounded errors. The preliminary experimental test for a small mobility on demand and public transport network shows the model provides a good solution quality.