A fuel control system delivers fuel to an engine cylinder and compensates for lost fuel. The fuel control system comprises a fuel dynamics module that determines a fuel dynamics model that is indicative of fuel behavior. The fuel dynamic module determines an inverse of the fuel dynamics model, receives a fuel command, and generates an adjusted fuel command based on the fuel command and the inverse of the fuel dynamics model. A lost fuel compensation module receives the adjusted fuel command and generates a final fuel command based on the adjusted fuel command and a lost fuel factor. A control module controls fuel delivery according to the final fuel command.