Tomori joined AC Milan initially on loan at the start of January with the club having the option to purchase him on a permanent basis at the end of the season.
The 23-year-old impressed in his first six months at the San Siro, making 22 appearances in all competitions to help AC Milan qualify for next season’s UEFA Champions League.
Milan will pay Chelsea £25m for Tomori’s services, with the central defender putting pen-to-paper on a four-year contract.
“AC Milan is delighted to announce the exercising of the option for the permanent transfer of Oluwafikayomi Oluwadamilola Tomori from Chelsea," a statement from the Serie A side reads.
“The English defender, who made 22 appearances and scored one goal over the last season, will continue to play with the Club until 30 June 2025.”
Chelsea's official website added: "Fikayo Tomori will complete a permanent transfer from Chelsea to AC Milan on 1 July.
"The defender spent the second half of last season on loan with Milan, but will make that move permanent next month after a deal was agreed between the two clubs."
Tomori came through the Chelsea youth ranks and spent time on loan at Brighton, Hull City and Derby County before making a first team breakthrough at Stamford Bridge at the start of the 2019/2020 season under Frank Lampard.
Tomori has won one cap for the England national team but is not part of the squad for the EURO 2020 tournament.