Both clubs, who are now at risk of a fine and a points deduction, were made aware of the alleged breaches on Monday and have now been referred to an independent commission to determine their sanctions.
Forest have become the third club in the top flight to be charged for flouting the league's financial rules.
Everton, meanwhile, have been hit with a second breach this term having already been punished with a 10-point deduction relating to the 2021/22 season.
"The Premier League does not have guidelines which prevent a club being sanctioned for alleged breaches in financial periods which have already been subject to punishment, unlike other governing bodies, including the EFL," an Everton statement read.
"As a result - and because of the Premier League's new commitment to deal with such matters "in-season" - the club is in a position where it has had no option but to submit a PSR calculation which remains subject to change, pending the outcome of the appeal.
"The club must now defend another Premier League complaint which includes the very same financial periods for which it has already been sanctioned, before that appeal has even been heard. The club takes the view that this results from a clear deficiency in the Premier League's rules.
"Everton can assure its fans that it will continue to defend its position during the ongoing appeal and, should it be required to do so, at any future commission - and that the impact on supporters will be reflected as part of that process."
Forest themselves stated that they acknowledge the Premier League's statement and they are hoping for a "speedy and fair resolution".
"Nottingham Forest acknowledges the statement from the Premier League confirming that the club has today been charged with a breach of the league’s Profitability and Sustainability Rules.
"The club intends to continue to cooperate fully with the Premier League on this matter and are confident of a speedy and fair resolution."
Premier League clubs are permitted to lose £105 million over a three-year period - or £35 million per season as part of the competition's PSR.
Forest, though, have their losses capped at £61 million due to them spending two seasons in the Championship.
Nuno Espirito Santo's side currently sit 15th in the table while Everton, who enjoyed a mini-revival after their points deduction, are 17th following a recent slump.
