The origin of the name comes from the family of Bois (de Bosco), which held the manor in the 12th and 13th centuries. For the village, the pronunciation is either boyce or boys. The village dates back to at least medieval times and in 1066 there were ten villagers.

Between 1348 and 1351 the Black Death killed approximately 30% of the population of England.

In 1381 the villagers of Theydon Bois took part in the Peasant’s Revolt having been hit hard because of a shortage of labour and food was scarce. The Statute of Labours meant that the peasants could not demand more money for their labour and therefore could not profit from the shortage. Poll tax to pay for the Hundred Years War had also been introduced as a one-off tax but it was so successful it was repeated three more times. This was the last straw for the peasants and in May 1381 riots broke out in Essex.

In Essex around 500 people were put to death without any form of trial.

Theydon Hall was the manor house until the early 17th century. The old parish church was nearby but was demolished in 1843.

The station was opened as Theydon as part of a branch line of the Great Eastern Railway on 24 April 1865. In December that year it received its present name. As part of the New Works Programme (1935–1940) the branch was transferred to London Underground, to form the part of the eastern extension of the Central line.

A notable characteristic of Theydon Bois is its almost complete absence of street lighting. Villagers have consistently voted against the installation of such lighting for decades, fearing that it would damage the traditional village ambience and require a rise in council tax. Only the approach to the tube station features a small number of lampposts.