Joining in September, Rowley will oversee a media team of 11 and an eight-strong public affairs department, reporting to GMC chief executive Finlay Scott.
On Tuesday, the GMC revealed that complaints against doctors had reached record levels, with 4,980 received in 2005, compared with 4,452 the year before.
The high-profile organisation was heavily criticised last year during The Shipman Inquiry.
Since May 2000, the GMC has carried out some of the most significant reforms since it was established in 1858. These include reducing the size of the ruling council from 104 to 35 members, changing the process for handling complaints about doctors, and ensuring the GMC is more accountable to parliament.
Rowley's new position absorbs some of the responsibilities of director of policy and public affairs Andrew Ketteringham. He is leaving this Friday to pursue other interests, including chairing housing association Paradigm Housing Group.
Rowley said: ‘I am looking forward to the challenge of ensuring the GMC's reforms are recognised, understood and engaged with.'
A former BBC and Sky journalist, Rowley joined Kennedy's staff in 2001.