[3] Brothertoft hamlet is mentioned in the Diocesan Return of 1563 (Deanery of Holland, parish of Kirton,) as having ten households.

[4] William Marrat, a local historian writing in 1814, noted that the traditional belief for the origins of the village name lay in a grant being awarded to two brothers in order that they could "inclose" (that is, separate and cultivate) the area from the surrounding fenland.

[5][6] In an addendum Marrat wrote that the place had been a vaccaria (or vaccary[7] - literally, a cow shed) of the abbey at Swineshead and had once been called Toft because of it relatively raised position above the fens.

[9] These are not definitive as another historian of the period, Pishey Thompson, pointed out that Toft was used as a name both for Brothertoft and Fishtoft in the late fourteenth century.

[10] The raised position did not exclude the area from flooding and, for example, in 1763 the villagers were forced to live in the upper stories of buildings due to the amount of water ingress.

[15] While the surrounding land belonged to Swineshead in medieval times, the manor of Brothertoft was worked by the Sempringham Priory.

[21] Sir Edward Carre, 1st Baronet of Sleaford,[22] was the owner in 1614 at which time his Brothertoft tenants were charged with the diking of part of South Ea as commoners in Holland fen.

[34] Prior to Frederick, the fenland often flooded to the point where boats had to be used for transport, and it was during his time at Brothertoft that drainage, and then enclosure began.

[35] Around 1767 the inhabitants of Brothertoft, who occupied 52 houses in the hamlet, were "most active" in rioting as a protest against the enclosure of Holland Fen.

Aside from general rioting and the removal of recently erected fencing, up to 200 people also played football on the land in an attempt to assert their historic rights, forcing Frederick to send men to guard the area.

[36] The situation led to serious injury and deaths, including the loss of an eye by a Captain Wilks who had been employed by Frederick to command the guard and who was shot.

[5][37] This common land had also traditionally been the scene of an annual fair, called the Toft drift, lasting a week from 8 July and attracting visitors from nearby villages and from Boston.

He sold his estate at Marnham, Nottinghamshire soon after and by the time he leased the estate and moved to Enfield, Middlesex in 1803 or 1805 had developed the rich loam soil into a profitable site for the cultivation of woad, assisted by new machinery, some of his own invention[5][34][38] and some developed by his bailiff and later steward William Amos[39] He began addressing his letters as being from Brothertoft Farm.

Marrat recounted in 1814 that Cartwright had sold off much of the land as separate farms, that the holding had consisted of around 880 acres (360 ha) and that the principal owners then had been Gee, T C Gerordot, C Dashwood, G Beedham and John Burrell.

[46] By the mid-1850s there were 123 inhabitants and the lands consisted of 900 acres (360 ha), with the principal owners being Gee, Herbert Ingram, Henry Rogers, George Cartwright and Mrs Barnsdale.

[52] The church, which is dedicated to St Gilbert of Sempringham, was a part of the chapelry of Kirton around 1837[53] and was owned by the lord of the manor,[5][37] it being at that time a chapel of ease.

[9] A former monk of Bardney, Otto Buttolle, was curate of Brothertoft in 1554, long before the surviving church records and when the living had an annual stipend of £3 6s.

[60] Five years later, in 1927 parts of the parishes of Holland Fen, Boston, Wyberton, Frampton, Kirton, Swineshead, Wigtoft, and extra-parochial land were transferred to the benefice of Brothertoft.

[55] Some form of provision for education existed in the mid-1700s as this is when an "obscure poet", William Hall, was taught in Brothertoft for a period of six months.