Although not mentioned in the Domesday book, records from 1272 show Trefonen as having an obligation to keep the lord's hounds . However, the village owes most of its current size to mining activity from the early 18th century until the last mine closed in 1891.During this period the resident populace became engaged in the extraction of the underlying coal, the quarrying of surface carboniferous limestone and its subsequent manufacturing use in a local pottery and brickworks. As these industries declined in the latter half of the 19th century local people returned to their agricultural roots and sheep and cattle rearing flourished.
Many of the village's local facilities were built to service the expanding working population of the 18th and 19th centuries and so the Malthouse was built in 1720, the Barley Mow public house in 1760, the Calvinistic Methodist Chapel in 1795, the All Saints parish church in 1821, the school house in 1825, and the Carneddau Independent Chapel in 1832. The village hall is the latest addition and was completed in 1991.
There is also now a brewery in the village which makes Offa's brew. This is located next door to the Barley Mow, and first opened in 2006.
Each year the village holds a Trefonen Hillwalking weekend over the Spring bank holiday, which includes a marathon race, horse trekking, various walks, social functions and with a Scarecrow competition as a highlight, which is held on the village green.
In 2008 the village set up a football team called Trefonen F.C., who play in the Welsh league system.