With the continuous development of the COVID-19 pandemic, the selection of locations for medical isolation areas has not always been optimal for the timely transportation of infected people, or those suspected of being infected. This has resulted in failure to control the rate of spread of infection cases in time. To address this problem, this paper proposes a co-evolutionary location-routing optimization (CELRO) model of medical isolation areas for use in major public health emergencies to develop a rapid location-routing scheme for epidemic isolation, including the selection of locations of medical isolation facilities per area and the optimal route per vehicle to each infected person. Specifically, this paper solves the following two sub-problems: (i) calculate the shortest transportation times and corresponding routes from any medical isolation area to any person infected or suspected of being infected, and (ii) calculate the location scheme for distribution of isolation areas. Different from previous studies, the vehicle operating characteristics and the interference of uncertainty of the traffic environment are considered in the proposed model. To find an appropriate scheme for location of medical isolation areas with the shortest travel times, a co-evolutionary clustering algorithm (CECA), which is a combination of some separated evolutionary programming operations, is proposed to solve the model. Various network sizes and uncertainty combinations are used to design some comparative tests, which aim to verify the effectiveness of the proposed model. In the experiment section, CELRO reduced travel time by at least 14% compared with other methods. This finding can provide an effective theoretical basis for optimizing the spatial layout of medical isolation areas or the location planning of new medical facilities.