The projects Benjamin Baker worked on with John Fowler were many and varied, and they included urban railways. The most significant of these were the early London Underground train lines. Fowler's Metropolitan Railway (now part of the Underground's Metropolitan and Circle Lines) is the world's first underground urban passenger train line.

When Baker joined Fowler's staff in 1862, Fowler was working on the construction of the Metropolitan Railway. It ran from Paddington to Farringdon Street via King's Cross (as it does today) and opened on 9th January 1863. He was also working on the St. John's Wood Railway, an extension of the earlier line. Both these lines were constructed using 'cut and cover' techniques with only the occasional short tunnel.

In 1869, Baker was appointed chief assistant engineer by Fowler for the construction of the Westminster to Mansion House section of the Metropolitan District Railway (opened December 1868), a further extension of the London Underground system. All the lines were served by steam locomotives. At this point Baker had already published various papers, the subjects of which included urban railways. The Metropolitan District Line work involved unusual difficulties that he later wrote about in The Actual Lateral Pressure of Earthwork (1881) and The Metropolitan & Metropolitan District Railways (1885).

The most innovative urban railway work undertaken by Fowler and Baker was the City & South London Railway, now part of the Northern Line. This is the first true 'tube’ line, consisting of a continuous tunnel dug with a tunnelling shield, a method that enabled the line to run below the city's network of pipes and sewers. The line had six stations and opened in November 1890. It was just over 5km in length and ran from the City of London under the River Thames to Stockwell, and is both the world's first deep-level tube railway of any length and Britain's first urban electric railway.

Fowler and Baker acted as consulting engineers on the City & South London Railway, with the South African engineer James Henry Greathead (1844-96) leading construction with Peter William Barlow (1809-85). Greathead designed the tunnelling shield. Baker, together with Basil Mott and David Hay, would also engineer subsequent extensions to the line done before 1907. Mott and Hay would later form the partnership that became Mott, Hay & Anderson.

Greathead and Barlow (and Barlow's son) had designed and constructed the Tower Subway tunnel (completed 1870), which also runs under the Thames. Tower Subway was orginally designed for a passenger cable car run from a stationery steam engine and is sometimes cited as the world's first tube railway. However, it ran for only three months and the subway soon became a foot tunnel, as it is today. The tunnel provided a template for the construction of the City & South London Railway — Greathead and Barlow senior had designed a wrought iron tunnelling shield to construct it.

In 1874, before the opening of the City & South London Railway, Baker published a paper entitled On Urban Railways in which he analysed the behaviour of the trains that used the underground system. The loads were heavy and the trains spent the greater part of their journeys accelerating and decelerating, using huge amounts of energy in the process. He put forward the idea of an undulating track. On the approach to a station, the track slopes up and on departure slopes down, aiding braking and acceleration.

This idea was not new. In the 1830s, Richard Badnall had enthused Robert Stephenson senior (1788-1837) — brother of George and uncle to Robert Stephenson — with the idea of an undulating track, and the two men went into partnership to promote it. In 1833, the idea reached trial stage on George Stephenson's Liverpool & Manchester Railway — the world's first passenger mainline. However, the idea was somewhat quashed by George.

So, it fell to Baker to be first to put the idea to practical use, which he did on his next major London Underground project, the Central London Railway, now part of the Central Line. This project proved so successful that it became the standard model of construction for urban railways across the world. Baker, Fowler and Greathead teamed up again for its construction. It opened in June 1900, and ran from Bank in the City of London to Shepherd's Bush in west London. Greathead again designed the tunnelling shield.

After Greathead's death in 1896, Baker worked jointly with W.R. Gailbraith on the engineering of the Baker Street & Waterloo Railway, also a 'tube' line. Now part of the Bakerloo Line, it opened in March 1906.