A spokesman said the departure was "very straightforward". There was no disagreement and no question of a pay-off to Mr Macpherson, who has been with 3i for more than 25 years.
Mr Macpherson said: "I shall not be retiring from business life but, at the age of 55, I am looking forward to new challenges. I shall be continuing my non-executive activities at Scottish Power and M&G Group."
A 3i source said: "He surprised quite a lot of people, but he could have stayed as long as he wanted." He is understood to have come back to his office this week after his 55th birthday on Sunday and told colleagues of his plan to depart in the summer. In the City, there was speculation that he would soon be in line for a non-executive chairmanship.
Mr Macpherson is to be succeeded in July as chief executive by Brian Larcombe, 43, the finance director. Martin Gagen and Peter Williams, joint heads of the UK investment business, are to join the 3i board as executive directors.
As well as earning a full pension from 3i, where he was paid pounds 392,000 in the year to March 1996, the accounts show that Mr Macpherson held share options which at last night's price would have given a paper profit before tax of just over pounds 2m.
Sir George Russell, chairman of 3i, said Mr Macpherson had steered 3i through a period of substantial change and development. "Many of the achievements are due to Ewen's vision, determination and persistence."