He will lead the organisation as it develops a new strategy for transforming the northern economy through better transport connectivity between the city regions, which is due to be published in March 2016.
An interim progress report on the new strategy will be released later this autumn.
TfN is also seeking to appoint an independent chair by the end of the year, with further plans to develop the organisation into a statutory body by 2017.
Brown, who will start his role within the next few weeks, is a highly experienced individual in the public transport and infrastructure sectors across the North of England.
He said of his appointment: “I’m delighted to be taking up this new role within TfN at a really exciting time for transport across the region and beyond. TfN will be at the forefront of delivering an integrated and holistic approach to transport in the North and I relish the opportunity to help shape and drive that forward.”
Prior to his appointment as chief executive/director general at Merseytravel, Brown headed up the South Yorkshire Passenger Transport Executive. He also led on the successful establishment of Rail North, which, similarly to TfN, brings together the northern authorities into a single organisation.
Transport secretary Patrick McLoughlin said: “I am delighted to welcome David Brown as CEO of Transport for the North. Given David’s wealth of experience in the region’s transport sector, he is perfectly placed to bring momentum to this vital new organisation.
“We set up TfN so the region can exercise real power and make its voice heard on how we can best invest in transport. That’s why we have given it £30m to take forward its work over the next three years. I look forward to working with David as together we transform northern transport and build the Northern Powerhouse.”