The ability to return a sample or small payload from International Space Station to a target on the ground will be in high demand in the near future. To satisfy this demand, several universities and NASA centers have been researching such a sample return system. One of the main features of the sample return systems is that they aim to deliver payloads at a designated position on the ground without using a thruster; thus, onboard guidance is essential in improving targeting accuracy of this passive system. This paper presents a trajectory analysis to develop a novel guidance scheme that can determine an optimal ballistic coefficient and phase transition states for the passive sample return system. Numerical simulations show that the ballistic coefficient of the system highly affects the orbital decay rate and the targeting accuracy. Hence, if the novel onboard guidance scheme optimizes the ballistic coefficient and phase transition state, high targeting accuracy can be achieved. Furthermore, an onboard surrogate model that can estimate the vehicle’s ballistic coefficient air density along the trajectory will assist the onboard guidance scheme in successfully guiding the sample return system.