The Germany international is currently sidelined with a hamstring injury, but has also now received treatment on his left knee.
Khedira missed most of last season after tearing the anterior cruciate ligament in his right knee, before suffering a strain in the other at the World Cup earlier this year.
A Real statement released on Wednesday read: "Sami Khedira, who is currently out injured with a left hamstring problem, has undergone an arthroscopic revision on his left knee.
"The procedure went successfully and was conducted by Dr Ulrich Boenisch at the Hessingpark Clinic in Augsburg with the supervision of Dr Jesus Olmo.
"The player will continue to be treated by the Sanitas Real Madrid Medical Services in the next few days."
Real host local rivals and Spanish champions Atletico Madrid in La Liga on Saturday.