Sir Alex Ferguson has lost his closest confidant at Manchester United after David Gill announced he will step down as chief executive in the summer to allow the club to "refresh" itself.

The United manager described the 55-year-old's departure as a "big loss". Ed Woodward, the executive vice-chairman, will replace Gill on 30 June although Gill will remain a director.

"Him stepping down is a big loss to me but the fact that he is staying on the board encourages me that the reason for his departure is heartfelt – that he believes it is time for the club to move on," Ferguson said. "If I could have found a way of persuading him to stay I would love to have done that. But he has made his decision and I respect him for it."

Woodward has overseen the recent burgeoning of United's global sponsorship deals, six of which were responsible for a 29% rise in commercial revenues, according to figures published by the club last week.

Gill predates the Glazer family's ownership, having joined United eight years before in 1997. Woodward, 40, may be regarded as less independent of the Glazers having been employed by them after impressing with the Briton's work for JP Morgan during their highly controversial leveraged buyout in 2005.

Woodward said: "This appointment is a great honour. I am particularly humbled to have the chance to work alongside the greatest manager in the history of the game. Alex's experience and track record are incomparable and I look forward to having the opportunity to support him in shaping his squad in the future and maintaining the club's position at the pinnacle of the sport."

Woodward's ability to act in the transfer market for Ferguson and to work alongside the Scot is how his tenure will be judged.

Gill, who hopes to join Uefa's executive committee in May, said: ""It has been the greatest privilege to serve Manchester United for 16 wonderful years – the last 10 of which as its chief executive.

"However, I have always been conscious of the fact that I was always just a temporary custodian of this marvellous institution.

"I am also of the view that all businesses need to refresh themselves with new management and ideas and after 10 years in charge, I believe it is appropriate for someone new to pick up the baton. And I hope to be able to make a contribution to the game on a wider national and European level."

On becoming chief executive in 2003 Gill forged a strong alliance with Ferguson that helped the club win four Premier League titles, three League Cups, one European Cup, one Club World Cup and an FA Cup.

Of his departure Ferguson said: "I have been at United for over 26 years and for 23 of those years, my boss has been one of only two men – Martin Edwards, who brought me to the club, and David Gill. I have enjoyed working with both.

"David has been a magnificent chief executive," Ferguson added. "Of course we have had a million arguments, but I have always enjoyed them because I know that David has two great qualities: he is straight and he always puts Manchester United first."

The experience in football of Woodward, a physics graduate from Bristol University, is limited to his eight years at United.

Gill said of Woodward: "I have worked with him for more than seven years and in that time he has built up knowledge of football matters, which will hold him in good stead for the future."