Appointed rector of Fordham, Essex, in 1642, Owen was made vicar at nearby Coggeshall in 1646 after preaching a notable sermon before Parliament the same year. At Coggeshall he came out in favour of Congregational autonomy in church government. His frequent preaching before Parliament led to his attachment to Cromwell, whose policies against the monarchy Owen began to support. After the execution of King Charles I by Cromwell's partisans in January 1649, Owen accompanied Cromwell on his military ventures to Ireland and Scotland (1649–50).

As chancellor of Oxford, Cromwell appointed Owen vice chancellor in 1652, a post he held until 1657. He was also dean of Christ Church Cathedral (1651–60) and was elected in 1654 to represent Oxford in Parliament, but he was later disqualified because of his clerical vocation. Reserved in his support of Cromwell, Owen opposed plans to offer the English crown to him and avoided participation in Cromwell's installation in the office of lord protector in 1653. Owen abandoned politics on the restoration of the monarchy in 1660, when the House of Commons removed him from his position as Christ Church dean.

Among his works are historical treatises on religion, several studies of the doctrine of the Holy Spirit, and defenses of Nonconformist, or Puritan, views. An edition of his Works, edited by W.H. Goold, comprises 24 volumes (1850–55).

Welsh epigrammatist whose perfect mastery of the Latin language brought him the name of “the British Martial,” after the ancient Roman poet.

Owen was educated at Winchester School and at New College, Oxford. He was a fellow of his college from 1584 to 1591, when he became a schoolmaster, first at Trelleck, near Monmouth in Wales, and then in about 1594 at Warwick, where he became headmaster of the school endowed by Henry VIII. He became distinguished not only for his mastery of Latin but also for the humour and point of his epigrams. Being a staunch Protestant, he could not resist the temptation of turning his wit against Roman Catholicism. This practice caused his book to be placed on the Roman Catholic Index Librorum Prohibitorum (“Index of Forbidden Books”) in 1654 and led a rich Roman Catholic uncle to cut him out of his will.

Owen's Epigrammata are divided into 12 books, of which the first 4 were published in 1606 and the rest at four different times. Owen frequently adapted the lines of his predecessors in Latin verse, and one such borrowing become celebrated as a quotation: “Tempora mutantur, nos et mutamur in illis” (“Times change, and we change with them”). After his death a monument was erected to his memory in St. Paul's Cathedral in London, where he was buried.