The area has been inhabited since Neolithic times. Until 1283 it was royal property, part (later centre) of the Gömör estate. In 1283 King László IV gave it to the Rátolth family (later: Putnoky family.) The family did a lot for the development of the town, but after the death of the dynasty founder Miklós a family feud began, and the inhabitants of the town and their other estates suffered a lot.
The Putnoky family had the castle of Putnok built between 1412 and 1427. During the Turkish occupation of Hungary the castle was destroyed, and in 1834 a manor house was built in its place.
The town developed a lot in the 19th century, still it lost its town status in 1881. After the Treaty of Trianon Hungary lost 92% of Gömör-Kishont county to Slovakia, and Putnok, as the largest village of the remaining part of Gömör-Kishont, became its county capital, but later this small county was merged with Borsod county, forming Borsod-Gömör-Kishont and after 1950 Borsod-Abaúj-Zemplén. Putnok lost its importance, in many senses its role was taken over by Ózd, still it got its town status back on March 1, 1989.