St Margaret's School in East Suffolk Road, Newington, has gone into administration, with receivers KPMG ruling it is no longer financially viable.
The closure will affect 100 members of staff and 350 pupils. The school, which is 110 years old, is due to close on 29 June.
Administrators said St Margaret's, which charges up to 2,628 a term, had no option but to close after several years of declining rolls and operating deficits. The value of its property portfolio had also been reduced in value by the recession.
Parents received an e-mail yesterday evening breaking the news, and the school said it was already in talks with other local private schools to find new places for pupils.
The school is understood to have had an average annual operating deficit of around 500,000 and turnover of 3 million. Pupil numbers had declined for at least five years, down from around 800.
Administrator Blair Nimmo said: "It's had operating deficits for a number of years, and quite substantial operating deficits. They have addressed these deficits firstly by trying to address the decline in pupils numbers."
There is thought to be no single reason for falling rolls at the school. Mr Nimmo said: "You don't need to lose too many pupils before you start falling into an operating deficit."
In a bid to reverse its financial decline, St Margaret's had started selling off parts of its property, but with its value reduced by the recession, this had not been sufficient.
Mr Nimmo said: "After a period of time, at least five years, of trading deficit that had failed to be addressed, you've got a school that was simply unviable."
Last month the Evening News reported that the school had frozen the pay of all staff for the next two years, prompting teaching union the EIS to consult its lawyers. The union said teachers had already experienced a year-long pay freeze, and thought a two-year extension could breach national pay agreements. School governors said that the pay freeze was necessary because the school had been hit by the economic downturn.
St Margaret's accepts boys up to junior level, with an all-girl senior school. The decision on closure had been timed to ensure it would not coincide with exams.
One parent of a two-year-old nursery pupil said: "I'm saddened, because it's a fantastic school. It has done our little one very well. It's just had an independent audit and came out as a centre of excellence in multiple sections. It's very sad – it's a real loss to Edinburgh."