This study aimed to explore the differences in detection between polymerase chain reaction (PCR) and rapid influenza antigen test (RIAT) in a population with influenza-like illness (ILI). A retrospective real-world study was conducted at 4 medical centers in China. The study included patients of all age groups who were suspected of having influenza and who underwent either RIAT or PCR testing. The positive detection rates of the two testing methods were compared during different epidemic periods, among patients with different disease durations, and between pediatric and adult patients. A total of 43,402 patients with ILI were tested, and 17,397 had positive results. The overall positive rate of PCR was higher than that of RIAT (68.3 % vs 33.8 %); however, there was no difference between the two methods during the start and end of the influenza season. The positive rate of RIAT in children (37.9 %) was higher than that in adults (27.2 %), whereas the positive rate of PCR in adults (72.8 %) was higher than that in children (59.5 %). The positive rate of RIAT was greater in the early stage (≤2 days) than in the later stage, whereas the positive rate of PCR was greater at 1-3 days than at other times.