The tunnel links the London Borough of Tower Hamlets with the Royal Borough of Greenwich, and forms part of the A102 road.

A tunnel in the Blackwall area was originally proposed in the 1880s. According to Robert Webster, then MP for St Pancras East, a tunnel would "be very useful to the East End of London, a district representing in trade and commerce a population greater than the combined populations of Liverpool, Manchester and Birmingham." By this time, all road bridges in London east of the ferry at Chiswick were toll-free, but these were of little use to the two fifths of London’s population that lived to the east of London Bridge. The Thames Tunnel (Blackwall) Act was created in August 1887, which provided the legal framework necessary to construct the tunnel. The initial proposal, made by Sir Joseph Bazalgette, called for three parallel tunnels, two for vehicular traffic and one for foot, with an expected completion date of works within seven years. It was originally commissioned by the Metropolitan Board of Works but, just before the contract was due to start, responsibility passed to the London County Council (LCC) when the former body was abolished in 1889 and Bazalgette’s work on the tunnel ended.

The original tunnel as built was designed by Sir Alexander Binnie and built by S. Pearson & Sons, between 1892 and 1897, for whom Ernest William Moir was the lead engineer. It was constructed using tunnelling shield and compressed air techniques and a Greathead shield (named after its inventor, James Henry Greathead). It was lit by three rows of incandescent street lights. To clear the site in Greenwich, more than 600 people had to be rehoused, and a house reputedly once owned by Sir Walter Raleigh had to be demolished. The work force was largely drawn from immigrants; the tunnel lining was manufactured in Glasgow, while the manual labour came from provincial England, particularly Yorkshire.

The southern entrance gateway to the tunnel, also known as Southern Tunnel House, was designed by LCC architect Thomas Blashill and was built just before the tunnel was completed. It comprises two floors with an attic.

The tunnel was officially opened by the Prince of Wales on 22 May 1897. The total cost of the tunnel was £1.4 M and 800 men were employed in its construction, during which seven deaths were recorded.

The tunnel has several sharp bends, in order that the tunnel could align with Northumberland Wharf to the north and Ordnance Wharf to the south, and avoid a sewer underneath Bedford Street.

Horse-drawn traffic was partially banned from the tunnel during peak hours in July 1939 and completely banned in August 1947. Pedestrians have been banned from using the Blackwall Tunnels since May 1969.

Due to the increase in motor traffic in the early 20th century, the capacity of the original tunnel was soon perceived as inadequate. In 1930, John Mills, MP for Dartford, remarked that HGVs delivering from Essex to Kent could not practically use any crossing of the Thames downstream of the tunnel. The LCC obtained an act to construct a new tunnel in 1938, but work did not start due to the outbreak of World War II. Construction eventually started in 1958 with preliminary work on the northern approach road.

It was opened on 2 August 1967 by Desmond Plummer, Leader of the Greater London Council.