The club, which is owned by its fans via the Exeter City Supporters Trust, declared a total profit of £1.642m for 2014-15, mainly due to the sale of midfielder Matt Grimes to Swansea City.
The deal in January 2015 for £1.75m, was a record sale for the club.
The profits came in the same year that the club were forced to get an emergency loan to pay players' wages.
In June 2014 cashflow problems meant the Professional Footballers' Association stepped in to pay the players and forced Exeter into a transfer embargo which was only lifted in August of that year.
The club's accounts also show that Exeter had a surplus of shareholders' funds of £761,000, compared to a deficit of £880,000 the previous year and reduced their cost base by almost 5%.
Exeter are hoping to redevelop St James Park after being given planning permission last month.
"The board have agreed in broad terms how the income from the transfer should be spent to improve the infrastructure strength of the club in line with its vision and underlying model and these plans are now being developed in detail for further presentation," said a club statement.

Miller served his ban from 2004 to 2006 after admitting using blood-boosting agent EPO early in his career.
The 39-year-old returned to the sport and has volunteered to educate Britain's young riders.
Technical director Shane Sutton said "nurturing an anti-doping culture" was at the heart of British Cycling.
Millar won stages in road cycling's three most prestigious stage races - the Tour de France, Vuelta a Espana and Giro d'Italia - and also won 2010 Commonwealth gold for Scotland in the road race time trial.
The Scot, who retired in 2014, is regarded as one of the sport's leading anti-doping campaigners.
Sutton added: "Having someone of David's calibre on board to support us in this education process is invaluable. He is readily available to share his well-rounded experiences as a professional cyclist to the young riders who aspire to succeed in their careers.
"David will work with the squad on a voluntary basis until the end of the month with a view to subsequently joining the team in a more official capacity."

Historic car specialists Fiskens said they placed the car for a "short time" outside their Kensington headquarters when two traffic wardens approached.
The firm said the wardens were "adamant" the 45-year-old vehicle should be given a £120 fine.
Kensington and Chelsea Council said it was "issued as it would in any case".
Acquisition specialist Rory Henderson said the company were always "super-careful" not to obstruct others who use the Mews when moving their vehicles around.
A council spokesman said the photographer agreed to move the Ferrari but "no attempt was made" within the "statutory five-minute observation period".
The car, a 1970 Ferrari 512M, is still in working condition and was recently raced at the Le Mans Classic.
According to Fiskens, it has a "remarkable history" having been raced in the 1970 and 1971 Le Mans races.
In 1977, it set a new record after Robert Horne drove the car 192mph over a flying mile.
Fiskens call it "a superb example of one of Maranello's finest sports competition cars".
League Two Exeter City made a profit of over £1.6m last year, according to the club's latest accounts.
[NEXT_CONCEPT]
British Cycling has revealed that David Millar, the former British road race champion who served a two-year doping ban, is mentoring its academy riders.
[NEXT_CONCEPT]
A rare Ferrari racing car worth about £10m was given a parking ticket after the owners rolled it into a Mews to take some photos.