The Premier League did not reveal the specifics of the club's alleged breach, other than saying it occurred in the period ending with the 2021-22 season.
However, Everton have posted financial losses in several recent seasons.
The Toffees denied wrongdoing and said they were "prepared to robustly defend" their position.
In their statement, Everton added: "The club strongly contests the allegation of non-compliance and together with its independent team of experts is entirely confident that it remains compliant with all financial rules and regulations.
"The club has, over several years, provided information to the Premier League in an open and transparent manner and has consciously chosen to act with the utmost good faith at all times."
In March 2022, Everton announced losses of £120.9m for the 2020-21 season.
That meant losses over a period of three years totalled £372m - more than three times the £105m permitted under Premier League rules.
The club said they remained "in a secure financial position" thanks to owner Farhad Moshiri - and blamed the Covid-19 pandemic for part of the losses.
Everton are also in the process of building their new Bramley-Moore Dock stadium.
They remain in a perilous position in the top flight, sitting 15th in the table - two points above the relegation zone.
Can Everton ever be great again?
Last year, rivals Leeds and Burnley wrote to the Premier League asking for Everton's accounts to be independently investigated, although they later dropped their threat of legal action.
The two clubs had been advised Everton complied with profit and sustainability rules after meeting with the Premier League.
In its statement on Friday, the Premier League said the commission would be independent of the league and its clubs, adding proceedings would be "confidential and heard in private".
There have been widespread protests against Moshiri and the Everton board by fans this season.
Last month, Manchester City were charged by the Premier League with more than 100 breaches of its financial rules following a four-year investigation.
City said they were "surprised" by the charges and were supported by a "body of irrefutable evidence"