From February, McIlheney takes on the leadership role at the magazine trade body that has been vacant since Jonathan Shephard's unplanned departure last September.
McIlheney's last high profile magazine appointment was when he resurrected Smash Hits in November (2009), presiding over the Take That special issue for Bauer.
The 49-year-old brings more than 25 years magazine and newspaper experience to the role, which began at local newspapers and weekly music magazine Melody Maker.
He joins the magazine association during a time of turmoil for both the industry at large and the association itself.
The approximately 3,000 consumer and business to business titles represented by the PPA are currently battling to retain their share of national ad spend and copy circulations in the digital age.
Meanwhile, another round of redundancies is currently taking place at the PPA's central London office, with up to 13 roles expected to change when the consultation period ends this month.
PPA chairman and managing director of BBC Magazines, Peter Phippen admitted it had been a "difficult period" for the PPA, but said he was delighted to welcome McIlheney as chief executive.
He added: "I'm excited that we are able to announce the appointment of Barry, who I am confident will rapidly restore the reputation of the PPA as one of the UK's best trade associations."
McIlheney, originally from Belfast, was appointed editor of Smash Hits in 1986 and went on to become managing director of Emap's Metro division, which publishes Q, FHM, The Face and Mojo.
He also launched FHM in France, and the men's weekly Zoo in the UK and Australia.