Last month the venue, which had a successful Fringe festival selling more than 36,000 tickets, was at a centre of a battle over its tax payments with HMRC.
HMRC lodged a petition with Edinburgh Sheriff Court in early August asking for an order that the company that runs the venue, Summerhall Management Ltd, be wound up and for the court to appoint a liquidator.
In a subsequent letter to performers, Rupert Thomson, the venue's programme director, acknowledged that the company was in dispute with the taxman over "the amount of tax we are due to pay", whilst allaying fears that performers would be paid for work this August.
The original HMRC petition stated that Summerhall Management Ltd was told by letter on July 11 that it owed a total of £202,848.
However, the popular venue, which has in its short history become one of the key venues of the annual festival, has now resolved its issues.
Sam Gough, Summerhall's general manager, said: "As planned, Summerhall has resolved all issues with HMRC.
"We're looking forward to moving into an exciting autumn programme of events, theatre and performance - and looking back on an incredibly successful festival for all our companies and artists many of whom we hope to welcome back in the near future."
It is understood the unpaid monies are the result of a "mix-up" or oversight connected to the rapid expansion of the venue.
This year the venue and its shows were among the brightest stars of the Fringe, with its ticket sales 275% higher than for the 2012 festival.
These sales did not include visitors to the free visual arts programme which included works by Michael Nyman, Fiona Banner, and Gregor Schneider's controversial Süßer Duft Edinburgh 2013, which featured a room of naked men.
Summerhall first opened in 2011 as an arts complex, and made its name on the Fringe with Hotel Medea in the same year.
The extensive B-listed Edwardian building, containing 500 rooms and more than 130,000 sq ft of space on a two-acre site, was sold by Edinburgh University to a private investor for around £3m that year.
The venue is not just a festival venue, as it is open throughout the year with visual arts shows, a bar, shop and The Royal Dick, the venue's pub.
A recent company statement said it was looking forward to welcoming back the Manipulate puppet festival and the International Science Festival, among many other forthcoming attractions.