Nepal boarders India and China and all three countries lie within the Central Asian Flyway for migratory birds. Novel influenza A H7N9 caused human fatalities in China in 2013. Subclinical infections of influenza A H7N9 in birds and the potential for virus dispersal by migratory birds prompted this study to assess avian H7N9 viral intrusion into Nepal. Surveillance of influenza A virus in migratory birds was implemented in early 2014 with assistance from the Food and Agricultural Organization (FAO). Of 1811 environmental fecal samples collected from seven wetland migratory bird roosting areas, influenza A H9N2 was found in one sample from a ruddy shelduck in Koshi Tappu Wildlife Reserve located in southern Nepal. Avian H7N9 and other highly pathogenic avian influenza viruses were not detected. This study provides baseline data on the status of avian influenza virus in migratory bird populations in Nepal.