Croatian midfielder Mateo Kovacic, 23, will join the Blues on a season-long loan as part of the deal.
Courtois was given the green light to leave after Athletic Bilbao goalkeeper Kepa was signed by Chelsea as his replacement.
Chelsea confirmed the transfer on the club website, which read: "Chelsea and Real Madrid have tonight agreed terms for the permanent transfer of Thibaut Courtois subject to the agreement of personal terms and passing a medical.
"Subject to the completion of the deal Mateo Kovacic will join the Blues on a season-long loan."
Real Madrid's club website confirmed that the medical will take place at 1pm in the honour box of the Santiago Bernabeu stadium.
The Spanish club added: "Subsequently, Courtois will step on the turf of the Santiago Bernabeu for the first time wearing the Real Madrid CF shirt and will attend media in the press room."
Belgium's No 1 ruffled a few feathers in the Chelsea camp this week as he skipped training and missed a meeting with Maurizio Sarri.
Courtois signed for the Premier League giants in 2011 from Genk for £8m.
He was pushing all summer for a return to Madrid – where he spent three seasons on loan at Atletico.
Courtois played 154 matches for the Blues, winning two Premier League titles – under Jose Mourinho in 2015 and Antonio Conte in 2017 – the League Cup in 2015 and the FA Cup last season.
He was also won the Premier League golden glove in 2017 and was named in the World Cup best XI earlier this summer.
After the transfer was confirmed, the 26-year-old posted a heartfelt farewell to the club and fans.
It read: "Hello CFC Family.
"With these few words I would like to express my heartfelt gratitude for the four fantastic years that have passed. Chelsea FC will always have a special place in my heart.
"I was only nineteen years old when the club showed a great belief in my abilities.
"The fact that such a big club was already following me was like a dream come true.
"The decision to first send me away helped my to go grow into a goalkeeper fit for Chelsea FC.
"When I returned, I was very happy to be part of one of the biggest teams in the world.
"I fulfilled a childhood dream playing in the Premier League, therefore I am really proud that we were able to win two Premier League title, a League Cup and a FA Cup!
"A huge thank you to all my teammates and technical staff over the past four years who I shared this success and amazing moments with, both on and off the pitch.
"The team would never be successful without the help of all the other members who are devoted to the players and the club, such as the medical department, kit men and all the others who I can’t thank separately!
"Last but not least I want to thank the fans for their great support over the years. I hope you understand that being closer to my kids was considerable in my decision.
"I wish you all the best for the future."
But Courtois deleted the post shortly after because he received so much abuse from furious football fans.
Kovacic will now showcase his talent in the Premier League after failing to cement his spot in Madrid's first-team.
The World Cup finalist has only started 37 league matches in the last three seasons for the La Liga giants.
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