The deal is worth around £355m and includes an option for a further two year extension.
Serco provided pre-launch consultancy and planning for the metro network from 2007 and began operating and maintaining the initial 10-station section of the Red Line when it opened in September 2009. The company has also operated the Green Line since it was inaugurated in September 2011 and became responsible for engineering and maintenance in 2012.
The automated metro currently carries around 120 million passengers per year and according to Serco has achieved 99.9% reliability.
Last month Serco was awarded a further contract by the RTA to operate Dubai's Al Sufouh Tramway.