Trains for Clacton-on-Sea usually originate at London Liverpool Street, while those for Walton-on-the-Naze typically start at Colchester (or Thorpe-le-Soken on Sundays).

The Great Eastern Main Line out of Shoreditch in London reached Colchester by 1843 and was extended to Ipswich in 1846.

The first short section of this branch line was built by the Colchester, Stour Valley, Sudbury & Halstead Railway to the port of Hythe, and opened for freight traffic on 31 March 1847.

c. cxix) to extend the line from Hythe to Wivenhoe, which opened on 8 May 1863 for both passenger and goods services from Colchester.

By the time the Wivenhoe extension opened the line had been taken over by the Great Eastern Railway (GER) who provided the rolling-stock in return for 50% of takings.

In the meantime, a short branch to a new station called St. Botolph's, located more centrally in Colchester, opened on 1 March 1866.

A section of the line between Frinton and Walton-on-Naze had to be re-sited in 1929 due to fears of coastal erosion on the original alignment.

[6] Between 1962 and 1992, services on the line were largely operated by a fleet of Class 309 electric multiple units which were specially designed and constructed for the route.