Benfica announced the sale overnight on Wednesday.
The price sum is stated to be 121 million euros (1,372,298,263 kroner), one million euros more than the player's buyout clause.
It is also said to be the highest total ever in English football.
According to Portuguese SIC, Fernández will fly to London later this afternoon.
Performance in Qatar
Chelsea gets Fernández in their squad for 8.5 years.
He was one of the big names during the World Cup in Qatar where he became a gold medalist with his Argentina and was awarded the prize for the tournament's best young player.
His fine play made several big European clubs look at him with interest.
The most eager was Chelsea, who managed to secure the player during a frantic final sprint on the final day of the transfer window.
The total, equivalent to nearly £106m is more than both the most expensive purchase (Jack Grealish who went from Aston Villa to Manchester City for £100m in 2021) and the most expensive sale (when Philippe Coutinho went from Liverpool to Barcelona for £105m in 2018) in Premier League.
Several shops
The London club has increased the wallet considerably this year, to speed up the game which has been limping lately.
In January alone, Chelsea have bought or loaned Mykhailo Mudryk from Shakhtar Donetsk, João Félix from Atlético Madrid, French defender Benoît Badiashile, winger Noni Madueke, right-back Malo Gusto, Ivorian David Datro Fofana and 18-year-old Brazilian Andrey Santos.
Chelsea received some addition to the coffers, but far from enough for the record purchase of Fernández, from the equivalent of the 150 million kroner that Arsenal were told to pay Chelsea for the Brazilian-born Italian midfielder Jorginho, a sale that was announced on Tuesday.
Gusto will also be on loan to Lyon for the rest of the season.