He joins as comms director on 1 August after three years in his current post, which is to be dissolved as the agency merges with other NHS bodies to form the Institute for Innovation and Improvement.
Mooney, a former BT marketing man, switched to the public sector after a six-month spell as an Army reservist during the Kosovan crisis in the late 1990s.
'After a tour of duty in Pristina I didn't feel like going back to the corporate world,' he said. Mooney takes over from Charles Skinner, who joined Haringey Council as head of comms last year (PRWeek, 5 November 2004).
DfT issues, such as road congestion and the proposed pay-as-you-go road toll, command a high position on the news agenda. The department was criticised earlier in the year for dissolving the Strategic Rail Authority, which cost £250m to set up.
The DfT has also struggled to distance itself from the Jo Moore scandal in 2001, when the special adviser suggested 9/11 was a good day to 'bury bad news'.
The move sparked a bitter row over advisers and led to the departure of Moore, transport minister Stephen Byers and comms director Martin Sixsmith.
Part of Mooney's challenge will be to restore confidence among comms staff, who at the time were accused of leaking Moore's email to the press.
In charge of a 50-strong department, he will report to DfT director-general of the delivery and security group Simon Webb.