The Northern and Eastern Railway opened a section of its authorised line from Broxbourne to join the ECR at Stratford on 15 September 1840.

The ECR tracks were originally set to a gauge of 5 ft (1,524 mm) on the recommendation of engineer John Braithwaite.

Braithwaite persuaded the directors otherwise on the grounds of additional cost but recommended the 5 ft gauge in an effort to reduce wear on locomotive parts.

This choice meant that the Northern & Eastern Railway who were planning to share the ECR line between Stratford and Bishopsgate were forced to adopt the same gauge.

[26] In 1854 the newly opened London Tilbury and Southend Railway served Stratford joining the main line at Forest Gate Junction a few miles north.

[23] It soon became apparent that congestion was a problem at Stratford and by 1856 permission was sought to build a line from Barking to Gas Factory Junction (Bow) which was opened in 1858.

Services from the North London line normally started from Victoria Park and ran through to Stratford Market.

[28] The North London Railway was also running through Stratford high level with two return trains per day from Hampstead Road (later renamed Chalk Farm) via Victoria Park and Forest Gate Junctions to Tilbury which commenced on 1 July 1855 and finished 30 September.

[31] The Loughton branch was extended to Ongar on 24 April 1865 and by 1874 there were a total of 40 trains each day (10 terminating at Loughton, 18 at Epping and 12 at Ongar) with most serving the newly opened Liverpool Street although a few peak hour services continued to serve Fenchurch Street.

Although one of the signal boxes had interlocking fitted soon after, the poor state of GER finances saw little further work until 1877 when a significant rebuilding of Stratford took place.

Another short-lived North London Railway service operated in September and October 1866, linking Chalk Farm with Barking (again routed via Victoria Park and Forest Gate Junctions).

[34] By 1889, traffic on the GER had grown to such an extent, that quadrupling the section from Bethnal Green to Bow Junction and from Maryland Point-Romford was proposed.

By the 1930s electric tramways were taking a lot of traffic from the railway and proposals were drawn up to electrify the lines from Liverpool Street to Shenfield using the 1500 V DC system.

[37] London Underground Central line services started on 4 December 1946, extended from Liverpool Street station in new tunnels after being delayed due to the Second World War.

[39] Prior to this date trains to and from Epping and Ongar had used the currently numbered platforms 11 and 12 and diverged from the Broxbourne line about half a mile north of the station.

[41] On 8 April 1953, 12 people were killed and 46 were injured as a result of a rear-end collision in a tunnel just to the east of Stratford station, caused by driver error after a signal failure.

[46][47] Initially the line used one of the south facing bays which had been built for the Fenchurch street via Bow Road service (but never used).

The Jubilee line opened to passengers on 14 May 1999 as far as North Greenwich station, and to Green Park and Stanmore in November 1999.

[60] From 6 November 2022, Elizabeth line services enter the central tunnel built as part of the Crossrail project, allowing direct trains to Heathrow and Reading via Paddington.

Work started in 2023 to add a new entrance to the station at its southwestern corner, adjacent to the Jubilee line concourse, allowing access to the Carpenters Estate.

However, since the diversion of the North London line from the low-level to the new high-level platforms these trains have changed the electrical system they use while at this station.

A short distance to the north of Stratford station (on the line to Cambridge) there were marshalling yards at Temple Mills.

There was a small goods yard north of the station on the east side of the line which occupied a constrained site.

The mainstay of traffic was domestic coal although shortly before closure in the 1960s the site was used as a reception point for concrete components for the building of tower blocks in Newham.

Since 13 December 2009 Southeastern began its full domestic high-speed service between London St Pancras, directly to Ebbsfleet International[76] and Ashford in Kent.

Passengers instead interconnect on high-speed trains travelling to either London St Pancras or Ebbsfleet in Kent, there are a number of other potential operators that may use the station for international services.

Both existing passenger subways have been extended north to connect with the ticket hall, and the abandoned subway at the eastern end of the station, which formed part of the old station complex, has been reopened and refurbished to allow interchange between platforms 3–12 and the new high-level platforms 1 & 2.

[80][may be outdated as of May 2022] The Hall Farm Curve link could be reinstated allowing a Liverpool Street to Chingford service via Stratford.