An autonomous vehicle (AV) implements a health protocol that may reduce pathogen transmission between users of the AV. The AV is equipped with a thermal sensor that captures a body temperature of a user. The AV compares the user's temperature to a threshold temperature, and if the user's temperature exceeds the threshold temperature, the AV performs checks to ensure that the user's planned trip follows current regulations or recommendations. For example, the AV confirms that the user is traveling between the user's home and a healthcare facility. If the trip is permitted, the AV enables the user to enter the AV. The AV may include a disinfectant system for disinfecting the passenger compartment or surfaces after the user exits the AV.