The data from a total of 200 children with suspected influenza virus infection were assessed at the febrile clinic of Women and Children’s hospital in Ganzhou of Jiangxi province from January 2018 to March 2019, and the patients were belonged to two groups (peramivir treatment group and oseltamivir treatment group). At the same time, 100 patients without special treatment were evaluated as the control group. We observed the patients’ fever relief time, pharyngeal pain relief time, nasal congestion relief time, runny nose symptoms relief time, days of hospitalization, days of medication, cost of medication, and adverse reactions in the three groups. We analyzed and compared the efficacy and adverse reactions of peramivir and oseltamivir in the treatment of children suspected with influenza. The recovery of body temperature, relief of cough, days of medication, and hospitalization period in the peramivir group were significantly shorter compared to the oseltamivir and control groups. The mean times to alleviation of fever in the three groups were 18.28 ± 17.74 h (peramivir group), 48.20 ± 34.28 h (oseltamivir group), and 72.56 ± 25.78 h (control group). The mean times to alleviation of cough in the three groups were 49.77 ± 27.58 h (peramivir group), 68.53 ± 32.54 h (oseltamivir group), and 59.38 ± 31.26 (control group). The cost of the peramivir group was significantly higher than that of the oseltamivir and control groups. The incidence of drug reactions in the peramivir group was significantly lower than that in the oseltamivir group. The rate of antibiotic usage in the peramivir group was significantly lower than that in the oseltamivir and control groups. Peramivir can significantly alleviate symptoms and reduce the use of antibiotics in children with suspected influenza. Peramivir has demonstrated good efficacy, high safety, and good compliance in treating children with suspected influenza infection.