Novel avian influenza A(H7N9) virus was isolated in fatal patients in Yangtze River Delta of China in March 2013. We aimed to screen the virus in febrile patients in a tertiary hospital in an area with confirmed cases. Throat-swab specimens collected from consecutive patients with fever (≥38°C) and flu-like symptoms from April 15 to April 25, 2013 were subjected to detect novel avian influenza A(H7N9) virus with real-time PCR. The clinical outcomes in the patients and close contacts were followed up. Of total 200 patients screened, one (0.5%) was positive for avian influenza A(H7N9) virus and 199 others were negative. The infected patient experienced respiratory failure and had diffuse infiltrates in the right lower lobe in chest CT images. He received symptomatic and antibacterial treatments as well as oseltamivir. His condition was substantially improved within three days after admission; avian influenza A(H7N9) virus was not detected after 5 days' antiviral therapy. The hemagglutinin inhibition test showed that the serum titers against avian influenza A(H7N9) virus increased from <1∶20 at the early phase to 1∶80 at the convalescent phase. Follow-up of 23 close contacts showed that none of them developed fever and other symptoms within two weeks. Our findings suggest that although the infection rate of avian influenza A(H7N9) virus in patients with fever and flu-like symptoms is rare, the screening is valuable to rapidly define the infection, which will be critical to improve the clinical outcomes.