The Belgium international has missed Chelsea’s last two games with an ankle injury, but he joined in with first-team training on Tuesday.
However, Chelsea have opted not to take risks with his fitness as the Arsenal game comes too soon and Courtois joins Alvaro Morata and Cesc Fabregas on the sidelines.
Willy Caballero will continue to deputise for Courtois, with the Argentine having started last week’s FA Cup third-round replay against Norwich and Saturday’s 4-0 Premier League victory over Brighton.
Morata has an ongoing back complaint which will see him miss out, while Fabregas is thought to still not be available through a hamstring injury, despite taking some part in Tuesday's training session.
Gary Cahill (hamstring) and Danny Drinkwater (ankle) will also likely return in some capacity, while Pedro is back from his one-game suspension after being sent off against Norwich.
With Chelsea one match away from a return to Wembley, manager Antonio Conte is excited by the chance of reaching another final within two years of joining the club.
"For me, my players, for the fans, it's an important target, especially for me," he said.
"In my first year or so I have the opportunity to win the Premier League, play the FA Cup final and now I can play another final in the EFL Cup.
"To have this possibility to play many finals in this country, it is very important for me. To play the final we must get past Arsenal, which is always a big challenge. Arsenal will also want to go to the final."