It also found that the fine levied on the club for exceeding spending limits was not disproportionate. British media reported in 2015 that the sum could be as much as 58 million pounds.
"We are understandably disappointed with the decision," QPR chief executive officer Lee Hoos said in a statement posted on the Championship club's website.
"We are currently examining our next steps, but we will be appealing."
The breaches occurred in the 2013-14 season when the West London club earned promotion to the Premier League by winning the Championship playoffs before coming straight back down the following year.
The EFL rules, which allowed losses of no more than eight million pounds, were aimed at preventing clubs over-stretching themselves and risking going bust to secure a place in the top flight.
"This decision vindicates the approach of the EFL board in defending this challenge," EFL chief executive officer Shaun Harvey said.
"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."
(Reporting by Shrivathsa Sridhar in Bengaluru, editing by Nick Mulvenney)
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