The 54-year-old hosted the ceremony from 2001 until 2006 when TV presenter Jonathan Ross took over but he is now taking back the role.
Speaking about his new appointment, Fry said: 'I had a marvellous time presenting the Film Awards for the first six years of the century.
'Hard as it may be for some characteristically sceptical Britons to believe, the BAFTAs have real kudos, reputation and cachet all over the world of film-making and I, old as I am, never cease to be shamelessly glamorised by the sight of so many legendary names who come every year as nominees and presenters.'
Ross, who is leaving the role, added: 'I have thoroughly enjoyed doing the Awards for the last five years and it is absolutely the right time for a change. I wish my old friend Stephen all the best and I'm sure he will do a fantastic job.'