Courtois did not report for Chelsea training this week in an attempt to force a move away from Stamford Bridge, prompting the Blues to scramble around for a replacement and swiftly identify Kepa as their preferred target.
Navas moved to Madrid from Levante in 2014 - the LaLiga powerhouse triggering the 31-year-old's €10million buyout clause.
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The time constraint on that deal is much less as Real have until the end of the month to sign players, while the early Premier League deadline only restricts buying and not selling.
After playing for Inter Milan and Real Madrid, Kovačić's stint at Chelsea will make him the fifth Croatian footballer in history to wear the jersey of the London club.
Real Madrid have confirmed that Courtois will undergo a medical on Thursday morning, before signing a six-year deal and being presented at 1pm local time.More news: Thomas Bjorn withdraws from PGA Championship with back injury
"The amount of the compensation established in the contract has been deposited".
There is also speculation that Chelsea could try to sign Atletico Madrid's Jan Oblak.
Courtois spent a total of three years on loan at Atleti, during which he laid roots in Madrid, and his young family still live there.
It means that Courtois is now free to travel directly from his Belgium home to the Bernabeu for his medical, ending the saga that started in the middle of the World Cup finals in June.More news: NASA mission to get closer to sun than ever before