The area has a long history of occupation going back to the Phrygians, Lydians, Persians and Ancient Romans. It was known as Koinon Gallicanon in antiquity. The Çatak Hamamı bathhouse dates back to the Roman times.
Göynük was absorbed into the Ottoman Empire in the early 14th century. In the late 19th and early 20th century, Göynük was part of the Kastamonu Vilayet of the Ottoman Empire.
Göynük has over 100 early 20th century Ottoman Empire period houses, these plus the even older mosques, tombs, fountains, and Turkish baths makes it a town of great historical interest, and an attractive location of narrow streets, with a pretty stream running through the centre. The victory tower on the hill at the top of the town and the old Ottoman mansion called "Müderrisoğlu Konağı" at the centre are important landmarks of Göynük.
Göynük was used as a location of films including Akrebin Yolculuğu by Ömer Kavur, El Yazısı and a number of Turkish TV series e.g. Aynalar and Rüzgarlı Bahçe.