Objective The purpose of this paper is to describe current practices of medical waste management, including its generation, investments, collection, storage, segregation, and disposal, and to explore the level of support from upper tiers of the government and health care system for medical waste management in rural China. Methods The authors draw on a dataset comprised of 209 randomly selected rural township health centers (THCs) in 21 counties in three provinces of China: Anhui, Shaanxi and Sichuan. Surveys were administered to health center administrators in sample THCs in June 2015. Results The results show that the generation rate of medical waste was about 0.18 kg/bed, 0.15 kg/patient, or 0.13 kg/person per day on average. Such per capita levels are significant given China’s large rural population. Although investments of medical waste facilities and personnel in THCs have improved, results show that compliance with national regulations is low. For example, less than half of hazardous medical waste was packed in sealed containers or containers labeled with bio-hazard markings. None of the THCs segregated correctly according to the categories required by formal Chinese regulations. Many THCs reported improper disposal methods of medical waste. Our results also indicate low levels of staff training and low rates of centralized disposal in rural THCs. Conclusions Medical waste is a serious environmental issue that is rising on the agenda of policymakers. While a large share of THCs has invested in medical waste facilities and personnel, it appears that actual compliance remains low. Using evidence of low rates of training and centralized disposal, we surmise that a lack of support from upper tiers of management is one contributing factor. Given these findings, we recommend that China’s policymakers should enhance support from upper tiers and improve monitoring as well as incentives in order to improve medical waste management.