The village once had a railway station on the Lanchester Valley Line, but this was closed in the early 1960s, with passenger service withdrawn in the late 1930s.

In medieval times Witton Gilbert was very important to the churchmen of Durham and became the place of a retreat or residence of the latter.

In the early 14th century, coal mining started in the parish from bell pits, however, the deposits were soon worked out.

Nearby collieries employed numerous workers, many of whom settled in Witton Gilbert, so that the population reportedly increased to about 4,400 people in 1896.

After Henry VIII's Dissolution of the Monasteries it was still occasionally used by the deans of Durham, but during the English Civil War it suffered major damage by Scottish troops.

Around 1175, Gilbert de la Ley, Lord of the Manor and tenant of the Bishop of Durham, financed the building of a leper hospital.

A medieval window frame carved out of stone can still be seen from Coach Lane, and the original entrance is now a doorway inside.