The Waterloo and City line will shut on Friday night for five months for "urgent upgrading".
The trains will be lifted by crane and transferred for refurbishment
The trains, which have not left the tunnels for eight years, will be moved by a 500 tonne crane for refurbishment.
The entire track in the tunnel between Bank and Waterloo will be replaced and the fire protection and other equipment will be renewed.
Tim O'Toole, of London Underground, said the work would mean quicker journeys and better trains.
The Waterloo and City Line is the shortest on the network with only two stops - Waterloo and Bank - in its one-and-a-half mile length.
It carries a relatively small average of 37,000 commuters on a weekday, and is 107 years old.
Some commuters said they were angry the line was being closed because it is already closed during weekends.
Stephen Hall, of maintenance firm Metronet, told BBC London: "The original plan was to close it for 18 months using weekends and some mid-week closures.
"By doing it in five months we're actually able to do some additional work and close it with lower risk.
"The refurbishment to the trains and some of signalling repairs and the refurbishment of the station platforms wasn't envisaged in the original plans. This allows us to do it."
Maintenance firms Metronet and Tube Lines must replace a third of all tracks on the network by 2010 under the Public Private Partnership.
Mr O'Toole said they had agreed to the request from Metronet to shut the line and improve reliability, passenger capacity, quicker journey times and a "smoother ride".
After consultation, LU said it had decided the line should close for five months so the improvements could be made at the same time.
London TravelWatch chairman Brian Cooke said: "If the Underground is to improve, then on occasions there will have to be short-term pain to deliver long-term gain."
The planned improvements are part of Transport for London's £10bn five-year investment programme, to improve and expand London's transport network.