BackgroundIn the battle against malaria in China, the rate of elementary and high school students’ awareness on malaria knowledge is an important index for malaria elimination, but only rare data is available. This study aimed to investigate the level of malaria awareness in students at elementary and high schools in malaria endemic areas of China, and to provide the baseline information for the malaria elimination.MethodsThis cross-sectional survey was conducted in 20 different malaria-endemic provinces in the first year of China’s National Malaria Elimination Programme (NMEP). A structured questionnaire was administrated to students at elementary and high schools enrolled. A total of 44,519 questionnaires were effective while 1,220 were excluded because of incomplete survey responses.ResultsMore than 60% of students were aware of malaria, but only 9,013 of them answered correctly to all five questions, and there were still 1,862 students unaware of malaria. There were significant differences of the awareness of malaria among different age groups, between male and female, between two different education levels.DiscussionThe study reveals that students at elementary and high school levels did not have adequate knowledge of malaria about biology, pathogenicity, transmitting vectors and preventive methods and so on at the beginning of NMEP in China. Further emphasis should be paid on health education campaigns in China to increase students’ public awareness of malaria about vector control, treatment, prevention.