The evolution of infectious diseases (IDs) poses a challenge to many ID physicians, who must either adapt or transition to another career track. This national cross-sectional study assessed the current working conditions and problems faced by ID professionals in China. A national questionnaire survey of ID physicians and their facilities throughout China was performed in May–June 2016 using stratified random sampling. A total of 156/300 (52.0%) ID departments and 1071/2250 (47.6%) physicians from 21 provinces participated in the survey. Overall, 151 (96.2%) of 156 hospitals had ID wards and 141 (90.4%) provided outpatient consultations. The average number of ID physicians per department was 10.32 ± 6.57. The ratio of patient beds to doctors was 5: 1, and the ratio of patient beds to nurses was 5: 1.85. Training in IDs was available in 126 (80.8%), and ID research was performed in 108 (69.2%), of the 156 departments. The main service provided by ID physicians was the management of legally notifiable communicable diseases. The annual income of 942 (88.0%) of the 1071 physicians was below $15 000. Of these physicians, 870 (81.2%) felt high or very high pressure in their work, whereas only 514 (48.0%) were satisfied or very satisfied with their jobs. The limited medical service provided by ID physicians is poorly aligned with current healthcare demands. Moreover, the heavy workloads, high stress, poor compensation and limited career prospects for ID physicians in China impede the continued development of specialists and places them in a career dilemma. ID physicians should work to develop and diversify the field and to enhance their capacities by learning new technologies and collaborating with other medical disciplines.