The Toffees are alleged to have broken the regulations during the 2021-2022 season.
Everton finished only four points above the relegation zone last season as Norwich City, Watford and Burnley dropped into the Championship.
The Merseyside club is embroiled in another fight to stay in the top flight, sitting in 15th place and only two points better off than third-bottom West Ham United, which has two games in hand on Sean Dyche's side.
Everton faces an anxious wait to discover if it will be hit with a points deduction.
A Premier League statement read: "In accordance with Premier League Rule W.82.1, the Premier League confirms that it has today referred an alleged breach of the League's profitability and sustainability rules by Everton Football Club to a commission under Premier League Rule W.3.4. The assessment period for which it is alleged that the club is in breach is the period ending season 2021/2022.
"Commissions are independent of the Premier League and member clubs. The members of the commission will be appointed by the independent Chair of the Premier League Judicial Panel, in accordance with Premier League Rules W.19, W.20 and W.26.
"The proceedings before the commission will, in accordance with Premier League rule W.82, be confidential and heard in private.
"Under Premier League rule W.82.2, the commission’s final award will be published on the Premier League's website. The League will be making no further comment until that time."