The diocese traces its roots in an unbroken line to the Pre-Reformation Diocese of Leicester, founded in 679. The see of Leicester was translated to Dorchester in the late 9th century, before taking in the territory of the Diocese of Lindsey and being translated to Lincoln. The diocese was then the largest in England, extending from the River Thames to the Humber Estuary. In 1072, Remigius de Fécamp, bishop under William the Conqueror, moved the see to Lincoln, although the Bishops of Lincoln retained significant landholdings within Oxfordshire. Because of this historic link, for a long time Banbury remained a peculiar of the Bishop of Lincoln. The modern diocese remains notoriously extensive, having been reportedly referred to by Bob Hardy, Bishop of Lincoln, as "2,000 square miles of bugger all" in 2002.
The dioceses of Oxford and Peterborough were created in 1541 out of parts of the diocese, which left the diocese with two disconnected fragments, north and south. In 1837 the southern part was transferred to other dioceses: Bedfordshire and Huntingdonshire to the Diocese of Ely, Hertfordshire to the Diocese of Rochester and Buckinghamshire to the Diocese of Oxford. Also in 1837 the county of Leicestershire was transferred from Lincoln to Peterborough (and became the independent Diocese of Leicester in 1927). The Archdeaconry of Nottingham was transferred to the Lincoln diocese at the same time.
In 1884, the Archdeaconry of Nottingham was detached to form a part of the new Diocese of Southwell.
By virtue of the 2009 scheme of delegation, whilst the Bishop of Lincoln exercises general oversight, the Bishops of Grimsby and of Grantham were seen as leaders in mission in the north and south of the Diocese respectively until that scheme lapsed upon the 6 April 2013 retirement of the Bishop of Grimsby, which was followed by a review of roles of bishops in the diocese. The suffragan See of Grantham was created in 1905, and the See of Grimsby in 1935. It would seem that the decision to not fill the suffragan see of Grantham was taken at some point, but later reversed.
Alternative episcopal oversight (for parishes in the diocese which reject the ministry of priests who are women) is provided by the provincial episcopal visitor, Norman Banks, Bishop suffragan of Richborough, who is licensed as an honorary assistant bishop of the diocese in order to facilitate his work there. There are also three retired bishops living in the diocese who are licensed as honorary assistant bishops: