The club have confirmed that they will appeal the verdict in an attempt to avoid what is thought to be the largest fine ever issued in sport.
QPR chief executive Lee Hoos said: “We are understandably disappointed with the decision and will be appealing.”
EFL chief executive Shaun Harvey, meanwhile, said: “This decision vindicates the approach of the EFL board in defending this challenge. The board will continue to enforce our rules on clubs to protect the interests of those that do comply.”
The fine is almost double that which Manchester City and Paris Saint-Germain were forced to pay for breaching FFP regulations three years ago.
Rules were enforced in the Championship in 2012 which permitted teams from making a loss of £8m, punishable with a fine for those that earned promotion.
After winning the Championship play-off final in 2014, QPR reported losses of £9.8m, considerably less than expected. Tony Fernandes, now the club’s co-chairman, and other shareholders had written off £60m in loans as an "exceptional item".
That was not deemed acceptable and they were issued with the £40m fine. A three-year battle ensued, and QPR have emerged unsuccessful.
Harvey added: “The board understand the challenges that this decision could create for our valued member club and will work with them, as and when the matter formally concludes.”