The present site was established as a place of worship in the Middle Ages, and a medieval church is mentioned in records going back as far as 1253 and 1291.
The church at Eglwysfach dates mainly from 1833. The lychgate is believed to belong to the earlier 1623 church though substantially rebuilt and enlarged, also in 1833. The original church is associated with a warlike legend that tells of the Northumbrian 6th century king, Edwin on a raiding expedition to this part of Britain. After his success in battle near to what is now Llandre he is reputed to be have founded a chapel at Eglwysfach.
RS Thomas, the internationally celebrated Welsh poet, was vicar at Eglwysfach between 1955 and 1967. An austere man, RS Thomas, with help from his artist wife, Mildred Elsi Eldridge, decided that the interior of his church should look dramatic. They took plaques off the walls, got rid of brass and had all the early 19th century pews and woodwork painted matt black. The interior retains this striking decoration.
Another writer who had a brief connection with the church was the satirical English novelist Thomas Love Peacock (1785-1866) who married Jane Gruffydd of Gryffydh, Maentwrog, in the church in 1820.