The present church was built in the first half of the 13th century, and it is believed to be on the site of an earlier building.

It contains a fine mural of 1872 on the east wall by Frederick Leach, of Christ in Glory surrounded by angels and saints.

The tower, designed by Charles Humfrey, is of cement render and initially had a spire; it was added in 1821–2, after a bequest by William Cole.

The church has the oldest memorial to a Mayor of Cambridge; the French inscription on the tombstone of Eudo of Helpringham who died in 1329 during his sixth mayoralty gives an early version of the modern form of the name of the town—'Caunbrege'.

In the north aisle there is a beam with a carved punning inscription of c. 1538, which is thought to indicate that Thomas Brakyn, who lived in the parish at the time, contributed to the cost; he is buried in St Clement's churchyard.

He was a tractarian who followed ritualistic worship at St Clement's, though he adhered strictly to the Book of Common Prayer.

His successor was the barrister-priest Fr James Tait Plowden-Wardlaw, Vicar from 1931 to 1941, who often published as 'Father Clement' or 'Clement Humilis' and maintained the Anglo-Catholic tradition.

[13] After a long vacancy, a viability plan, drawn up by a working group from the congregation, was accepted by the Bishop of Ely in December 2013.

[19][20] In 2022, bellringing group, the Society of Cambridge Youths, installed a ring of bells at the church.