Courtois conceded twice in the first half at Santiago Bernabeu as Madrid struggled against the Belgian side in the UEFA Champions League.
The Belgium international did not emerge for the second half, with Alphonse Areola sent on in his place, and Madrid came back to draw 2-2.
Madrid coach Zinedine Zidane said Courtois "wasn't well and couldn't continue" in the aftermath of Wednesday's (AEST) Group A game.
But after local media reported Courtois has been affected by anxiety, Madrid hit back with a strong rebuttal in an official statement.
"In relation to certain information about our player Thibaut Courtois, Real Madrid wants to state the following," the statement read.
"1. That our player has never been diagnosed with an alleged anxiety problem and therefore, that information is absolutely false.
"2. That Thibaut Courtois has been diagnosed and treated for acute gastroenteritis with dehydration and electrolyte imbalance, which made it impossible to complete last Tuesday's game against Bruges.
"3. The player currently responds favourably to the treatment."
Madrid faces LaLiga surprise package Granada at home on Sunday (AEST) and it is unclear whether Courtois will be available.