In February 1518 he was installed prebendary of Heydour-cum-Walton in the diocese of Lincoln, and before 1522 he was rector of Houghton-le-Spring, Durham, and held the prebend of Eveston, in the collegiate church of Lanchester, in the same county.
On Thomas Wolsey's accession to the see of Durham he confirmed Franklyn in the chancellorship, with power of appointing justices of the peace, coroners, stewards, bailiffs, and other officers; and the chancellor made himself useful to the bishop in devising plans for increasing the revenues of the diocese.
On 17 December 1536 Franklyn was by patent appointed dean of Windsor, and in 1540 he exchanged his Lincolnshire prebend for the rectory of Chalfont St. Giles, Buckinghamshire, the parsonage attaching to which he afterwards let to John Storie.
As dean of Windsor he assisted at the christening of Edward VI and the funeral of Lady Jane Dudley, and his signature is affixed to the decree declaring the invalidity of the marriage of Henry VIII with Anne of Cleves.
A large number of letters addressed by Franklyn to Wolsey, Thomas Cromwell, and others were preserved, in the Public Record Office and the British Museum.