Dr Jon Lamonte, chief executive of Tube Lines, a subsidiary of Transport for London, will become head of Transport for Greater Manchester in January.
Greater Manchester Combined Authority said Lamonte will succeed David Leather, who has been seconded from Ernst & Young since 2006.
Tube Lines has an annual turnover of between £600m and £700m and employs 2,500 people. The company is responsible for operating the Jubilee, Northern and Piccadilly lines. Prior to this Lamonte worked for the Royal Air Force and Ministry of Defence.
Lamonte said: "Maintaining a real hard-edged focus on the delivery of the £2bn capital programme is vital as is its role in boosting the growth of the Greater Manchester economy. At the same time, putting the customer first has to be a top priority, delivering safe, reliable and efficient services that we can all take pride in. Everyone has told me what a great place Manchester is to live and work and I can't wait to make a start."
At TfGM he will oversee a £2bn investment programme that includes the ongoing expansion of the Metrolink network, increased rail capacity, the planned introduction of smart ticketing and integrated fares, four new transport interchanges and bus priority measures. The programme is forecast to create 21,000 extra jobs by 2021.
Lord Peter Smith, chairman of GMCA, said: "Transport for Greater Manchester has achieved much in recent years under the leadership of David Leather. But many challenges remain, not least achieving the rail improvements which will help Greater Manchester realise its potential. Jon Lamonte's leadership and vision will be crucial to meeting these challenges in the years ahead."
GMCA is also working with other local authorities across northern England in seeking to secure control over the Transpennine and Northern rail franchises.
Cllr Andrew Fender, chairman of the TfGM Committee, said: "The work of TfGM touches on the lives of everyone in Greater Manchester so it was important we found the right person.
"Jon Lamonte has an outstanding track record in leading the delivery and supervision of large-scale and complex projects and we believe he is the ideal person for this broad and significant job.
"He joins TfGM at an exciting time. David Leather and his team at TfGM have built strong foundations for a transport revolution in Greater Manchester, which is well underway, but it's going to be a long journey and not without obstacles to be overcome along the way."
Lamonte will have a starting salary of £265,000, rising to £275,000 in January 2014 and £285,000 in January 2015.