On the main line, Limehouse is located 1 mile 58 chains (2.8 km) from Fenchurch Street and the following station is West Ham; on the DLR it is between Shadwell and Westferry in Travelcard Zone 2.

At that time, the Commercial Railway had a separate station named Limehouse one stop to the east.

The station was opened on 6 July 1840 by the Commercial Railway,[7] located in the parish of Stepney within the hamlet of Ratcliff.

[8][9] On 28 September 1850 an extension was opened from Stepney to Bow, to join the LBR with the Eastern Counties Railway (ECR).

A further accident in 1879 saw the Board of Trade inspector recommend the re-siting of the signal box which was duly provided in 1880.

In 1895 the fourth line towards Fenchurch Street was opened which helped reduce the number of conflicting moves between trains and thus the risk of accidents.

A few goods trains used the Blackwall route but the LBR platforms were demolished in circa 1936[7] and the junction simplified.

[15] The route to Stratford via Bow Road was electrified in 1949 and it was at that time that the former GER suburban services ceased operating leaving Stepney East served only by trains to the former LTSR destinations.

[19] Prism was bought out by National Express who named the franchise c2c in 2003 and continue to operate the station.

[20] Since the opening of the DLR, Limehouse has become a well-used interchange for Essex and east London commuters who work in the Canary Wharf area, but the two viaducts remained separate, resulting in an awkward interchange between the DLR platforms and the National Rail platforms, as passengers had to pass down and then up flights of stairs.

At the same time as the bridge was being built, other improvements were made, including readying the station for three-carriage operations on the DLR and the construction of an additional eastern entrance, with lifts and stairways for platform access.

There was a short-lived passenger train service between Blackwall and Palace Gates (via Stratford and Seven Sisters) which operated from 1 September 1880 until 1 March 1881.

Some special excursion trains also used the curve about this time running from Blackwall to Southend and Southminster on summer Sundays in 1890 and 1891.