Centuries ago Payyanur was part of famous Ezhimala Kingdom and was ruled by King Nandan.Later Ezhimala came under regime of the Chera Dynasty and thereafter the Mooshaka Dynasty. A village south of Payyanur, Ramanthali was the headquarters of the Mooshaka Dynasty. Later during the regime of the Kolathiri Dynasty Payyanur was a part of Kolathu Nadu ruled by the Kolathiri Rajas based in Chirakkal near Kannur. During the British Rule, Payyanur was part of the Chirakkal Taluk. Soon after receving independence from British, and the formation of Kerala state in 1957, Payyanur was taken away from Madras state and joined to Kerala state. Since then Payyanur is administered by elected members of Payyanur Panchayat/Municipality.