Emlyn was born at Stamford, Lincolnshire. He served as chaplain to the presbyterian Letitia, countess of Donegal, the daughter of Sir William Hicks, 1st Baronet who married (1651) and survived Arthur Chichester, 1st Earl of Donegall.
Emlyn was then chaplain to Sir Robert Rich, afterwards (1691) becoming colleague to Joseph Boyse, presbyterian minister in Dublin. From this office he was virtually dismissed on his own confession of unitarianism, and for publishing An Humble Inquiry into the Scripture Account of Jesus Christ (1702) was sentenced to a year's imprisonment for blasphemy and a fine of £1000. More than two years later (thanks to the intervention of Boyse), he was released in 1705 on payment of £90.
He is said to have been the first English preacher definitely to describe himself as "unitarian," and writes in his diary, "I thank God that He did not call me to this lot of suffering till I had arrived at maturity of judgment and firmness of resolution, arid that He did not desert me when my friends did. He never let me be so cast down as to renounce the truth or to waver in my faith." Of Christ he writes, "We may regard with fervent gratitude so great a benefactor, but our esteem and rational love must ascend higher and not rest till it centre in his God and ours."
Emlyn preached a good deal in Paul's Alley, Barbican, in his later years, and died in London in 1741.
Emlyn's Works were collected by his son Sollom Emlyn in 1746, 3 vols., called the "fourth edition", but this refers only to the included Collection of Tracts (1719; 1731, 2 vols.; 1742, 2 vols.). His first publication was The Suppression of Public Vice, Dublin, 1698, (sermon on 1 Sam. ii. 30). Among his other pieces are:
In 1823 Jared Sparks published at Boston, U.S., a selection from Emlyn's works, with memoir. Answers to Emlyn's positions were furnished by Stephen Nye (1715), Jacques Abbadie (1719), C. Alexander (1791), and Aaron Burr Sr., president of the college in New Jersey (1757), on occasion of an American edition (1790) of extracts from the 'Humble Inquiry.'