Cardoe takes over from Steve Carroll, who had been in the top role at Athena since 2008 but was moved to a new role of senior consultant earlier this month.
The move is thought to be the first part of a wider restructure at the agency, with further details expected to emerge later this year.
Cardoe was hired by Athena in August on a part-time basis, but under the new arrangements she will now take over the day-to-day management at Athena.
Prior to Athena, Cardoe held comms and PR director roles at Synergy and the Institute of Cancer Research, and spent two years as MD at Ogilvy Healthworld PR's New York operations.
Carroll succeeded long-standing MD Cherry Wood in 2008, who resigned to launch her own agency.
Carroll previously headed FleishmanHillard's pan-European healthcare practice, having also worked as a GP.
Industry sources suggested that the Athena brand was due to be wound down later this year. Athena chairman Mike Lane told PRWeek that the group had just undertaken a strategic review of Lane, Earl & Cox Advertising and Athena Medical PR.
He said: 'The idea of separate silos of creative, PR, medical education and digital offerings should give way to a more integrated approach.'
But he played down speculation that the PR agency would be closed, insisting: 'We may change the business model, but Athena is an important part of our future strategy.'