Striped skunks (skunks) are susceptible to respiratory infection by influenza A viruses (IAV). As they are common synanthropes, maintenance of IAV in skunks could provide a source of infection for humans. We previously studied the nasal turbinates, lungs and faeces of 50 free-ranging skunks for the presence of IAV and identified two individuals with influenza A(H1N1)pdm09 infection during the 2009/2010 and 2013/2014 flu seasons. Subsequent to publication of that study, ferrets were shown to preferentially replicate and harbour A(H1N1)pdm09 in the soft palate, a site which had not been investigated in the skunks. From March 2015 to May 2016, we surveyed a convenience sample of 80 free-ranging urban skunks for IAV in soft palate, nasal turbinates and lungs. The newly emergent influenza A(H1N1)pdm09 clade 6B.1 was detected at all three sites in one skunk with acute rhinitis in February 2016. Clade 6B.1 was the dominant clade in circulation during the 2015/2016 flu season. As the skunk was detected at the height of flu season, reverse zoonosis was considered the most probable source of infection.