The FA said the conduct the charges relate to spans 2009 to 2022, when the Blues were owned by Russian billionaire Roman Abramovich, and primarily relates to events that occurred between the 2010-11 to 2015-16 seasons.
The FA said the west London club had until September 19 to respond to the charges.
Chelsea issued a statement saying the club was "pleased to confirm that its engagement with the FA concerning matters that were self-reported by the club is now reaching a conclusion".
"The club's ownership group completed its purchase of the club on May 30, 2022," the statement continued.
"During a thorough due diligence process prior to completion of the purchase, the ownership group became aware of potentially incomplete financial reporting concerning historical transactions and other potential breaches of FA rules.
"Immediately upon the completion of the purchase, the club self-reported these matters to all relevant regulators, including the FA.
"The club has demonstrated unprecedented transparency during this process, including by giving comprehensive access to the club's files and historical data.
"We will continue working collaboratively with the FA to conclude this matter as swiftly as possible. We wish to place on record our gratitude to the FA for their engagement with the club on this complex case, the focus of which has been on matters that took place over a decade ago."
In August 2023, Premier League chief executive Richard Masters said his organisation was investigating "historic" financial issues that the club had self-reported to the Premier League and to the FA.
A spokesperson for Abramovich has been contacted for comment.
In July 2023, Chelsea agreed a resolution with European football's governing body to hand over 10 million euros ($A17.7 million) after owning up to "incomplete financial reporting" under Abramovich.
UEFA said it had been "proactively" approached with the information by Chelsea's new ownership group.
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