Francis Johnson (1563–1618) was an English presbyterian separatist minister, pastor to an English exile congregation in the Netherlands.
He was the elder son of John Johnson, mayor of Richmond, North Riding of Yorkshire, born at Richmond and baptised there on 27 March 1562. George Johnson was his brother. He matriculated at Christ's College, Cambridge, graduated B.A. 1581, M.A. 1585, and was elected fellow before Lady day 1584.
He was a popular preacher in the university, and a follower of the independent presbyterianism advocated by Thomas Cartwright. On 6 January 1589 he expounded this view in a sermon at Great St. Mary's, Cambridge, claiming that church government by elders is jure divino. With Cuthbert Bainbrigg, also a fellow of Christ's, accused of factious preaching, he on 23 January came up before Thomas Nevile, the vice-chancellor.
Refusing to answer on oath to the articles of accusation, Johnson and Bainbrigg were committed to prison. Johnson gave in written answers which set out his views, but again on 13 March and 18 April declined the oath. Bail was offered by Sir Henry Knevett and Sir William Bowes, but was rejected by the authorities. On 22 May Johnson and Bainbrigg addressed a letter to Lord Burghley, the chancellor; but the vice-chancellor laid the case before the court of high commission, which directed the vice-chancellor and heads to proceed at discretion. A form of recantation was given to Johnson on 19 October and he was required to read it in the pulpit of Great St. Mary's. He made an unconvincing retractation and on 30 October he was expelled from the university. He claimed a right of appeal, and refusing to leave; he was in December again in custody and vainly petitioning Burghley, backed by fellows of colleges.
Johnson went to Middelburg in Zealand, where he became preacher to the English merchants in the Gasthuis Kerk, with a stipend of £200. In 1591 'A Plaine Refutation' of the claims of the establishment, by Henry Barrow and John Greenwood came Johnson’s way. It was an answer to George Gifford, and had been sent privately in 1591 to Middelburg to be printed. The edition was burned by Johnson on the magistrate's authority for suppressing it.