The church, dedicated to St. Botolph, is one of the largest in Rochester Diocese and was a wealthy living, frequently held by an absentee incumbent. It dates from the early 14th century in the decorated Gothic (with the exception of the two nave windows, which are perpendicular), and consists of a six bay nave with north and south aisles and chancel. The tower was built in 1717 inside the one that fell in the previous century. At the south west corner is evidence of the original Anglo Saxon church, with long and short work on the quoins. Inside part of the arcade is 13th century work. Perhaps the most interesting interior feature is the chancel screen that is early 14th century, the same period as the church. It retained its solid wooden doors until about 1830.

The chancel arch and the harsh sedila in the chancel are both the work of E.W. Godwin in 1862, but there is an attractive piscina and sedila in the south side, which are original, although the sub deacon's seat was damaged in 1790, when W.H. Burch built a family pew here with 'a warming machine'. The altar dates from 1922 and the screen was erected in 1937 as a memorial to George Snelling and Charles Kean. The floors of both nave and chancel were raised during the Victorian restoration, and the well known brass of Peter de Lacey (13 75) lost its canopy and now has a small modern border. St. Botolph’s at one time had at least 13 brasses, but of these only three remain, the other two being William Lye (1391) and William Rikhill and his wife Katherine (1433). All have been moved and mutilated.

The chancel was refurnished and fitted between 1861 and 1879. The Victorian stained glass was restored and rededicated on St. Botolph's day 1992 after six years' work at a total cost of £30,000. According to Martin Harvison, the author of Victorian Stained Glass (1980), the east window is one of the major 19th century windows, being a fine example of collaboration between E.W. Godwin, the architect, J. Miller Allen and Favers and Barnard, the glaziers. It was completed in 1863 as a memorial to Prince Albert. It was designed by Miller Allen (for a detailed description of this and the other Victorian windows at Northfleet see The Windows of St. Botolph', Northfleet by Michael Camp and Keith Hill, 1992).
The window tracery was restored in 1852 by Brandon and Ritchie, who seem to have copied what was there with the exception of the second window from the east on the north side. The east window of the south side is a good example of Kentish tracery with split cusps.

The St. Botolph's National School was opened in 1838 and was situated on the south side of the churchyard, adjoining the chalk pit. On 1 February 1869, the Infants' School was opened. Previously all ages had attended the one school, and the infants paid 2 pence per week to attend. The school continued unchanged until February 1936, when the eleven-year-old senior boys and girls left to attend the new Secondary Schools. From 1936, the school was a Primary (Mixed) School. It was not until June 1938 that electric light was installed. In 1977, a new St. Botolph's school was built on a new site in Dover Road that offered superior facilities set in large grounds.