Leicester, who were relegated to the Championship last season, had failed to submit their audited financial accounts, the Premier League said in a statement.
"The alleged breach relates to the assessment period ending Season 2022/23 when the club was a member of the Premier League," the statement said.
"The proceedings will be conducted in accordance with a timetable to be set by the independent commission."
Leicester said they were surprised and disappointed by the league's decision to charge them despite them not being a Premier League club.
"LCFC remains willing and eager to engage constructively with the Premier League and the EFL to seek the proper resolution of any potential charges, by the right bodies, and at the right time," they said in a statement.
"The club continues to take careful advice about its position and, if necessary, will continue to defend itself from any unlawful acts by the football authorities, should they seek to exercise jurisdiction where they cannot do so."
If found guilty, Leicester could become the third club to face a points deduction for breaching Premier League spending rules, after Everton and Nottingham Forest.
Defending champions Manchester City were also referred to an independent commission last year over more than 100 alleged breaches of finance rules. No verdict has yet been reached in that case.
Leicester are second in the Championship, equal on points with leaders Leeds United, as they pursue promotion back to the Premier League.
