McIlheney, a former Smash Hits editor renowned for his high energy levels and commitment to print media, takes up the role on 1 February, replacing Jonathan Shephard.
Shephard's exit in September last year followed an 18-month tenure that was subject to heavy criticism.
He was rounded on for his structural changes, particularly the scrapping of PPA's active marketing and research division, led for more than 15 years by Phil Cutts - now at The Economist Group.
Announcing his departure, PPA chairman Peter Phippen, said the "next phase of development should be conducted under a new chief executive".
Enter men's publishing maestro McIlheney. Not an obvious choice for some, but these are interesting, unchartered times for the magazine industry. When Media Week broke news of the PPA appointment yesterday, he received the immediate backing of some high profile magazine executives.
Evelyn Webster, chief executive of IPC, said: "I think this is an excellent appointment. His knowledge of print is second to none and he has a terrific enthusiasm for print."
McIlheney's CV details more than 25 years in publishing, including roles as editor of Smash Hits and film title Empire, while his spell at Emap included responsibility for brands such as Q and The Face.
He has also held editorial positions with Zoo and FHM, and has recently lent his experience to trying to u-turn the fortunes of downmarket title, the Daily Sport.
Webster added: "I think the PPA has been guilty of losing focus and momentum on important issues. It needs fresh energy to focus on the issues that are impacting business-to-business and consumer publishers, such as digital and diversifying revenue streams, but retaining a focus on print."
Mike Soutar, chief executive of ShortList Media, publisher of ShortList and Stylist magazine, said: "Barry is an out-and-out print man. He has print running through his veins. I can't imagine a better ambassador."
Soutar added that the structure of the PPA, which is chaired by BBC magazines managing director Peter Phippen, is fundamentally sound despite its recent lack of leadership, as it has operated without a chief executive or deputy chief executive.
Despite the tough economic climate, the success of the FIPP World Magazine Congress in May last year, which was hosted by PPA and attracted 900 delegates from 57 countries, highlights the important role the association can play in today's changing marketplace.
The trade body also won a long-running battle with the Office of Fair Trading to prevent the magazine distribution system being referred to the Competition Commission. And there are plenty of more battles to be had on behalf of the embattled magazine industry in the immediate future.
Announcing yesterday's appointment, outgoing chairman Phippen appeared to sum up the general feeling when he said: "After a difficult period for the PPA, 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."
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