McGuinness, formerly a senior and highly respected ad man, joined Freuds in the summer of 2014 after leaving BMB, the advertising agency he co-founded. Before that, he spent many years as a senior executive at TBWA\London.
Since joining Freuds he has focused on a series of acquisitions such as Brew PR in America. He continues to be a director of the Seven Dials PR agency, which is run by former Independent editor Simon Kelner.
McGuinness is credited with strengthening Freuds' top team and striking new partnerships with Virgin Money, McCain and London & Partners. However, under his leadership Freuds has also lost the flagship Asda account, this summer, PepsiCo’s corporate work and the HomeAway business.
It is understood McGuinness will now focus on his own ventures, but will continue to serve as an adviser to Freuds, with a specific focus on acquisitions and nurturing the businesses in which the agency has recently invested.
In a note to staff this afternoon Freuds founder and chairman Matthew Freud said: "After two years at the helm of Freuds, and having recently completed his course at Harvard Business School, Andrew McGuinness is today stepping down from his role as CEO. He has guided the agency through one of its most significant periods of transformation and growth, culminating in this year being on track to be our most successful ever."
Freud added: "Andrew has been instrumental in strengthening the top team and directing the agency’s new business strategy, resulting in exciting partnerships with Virgin Money, McCain, London & Partners and many others."
McGuinness said: "It's been a terrific experience: leading freuds back into the US, lots of new business and helping achieve the best performance in 31 years. I learnt a lot at Harvard but even more from Matthew."
It is not yet clear how, or indeed whether, Freud will replace McGuinness.
Previous Freuds chief executives include Nicola Howson, Fiona Noble and Nick Wiszowaty.