It had been reported earlier this week that Atletico would need to pay Chelsea a sizeable fee in order for Courtois to feature against them in the latter stages of the Champions League.
Before the two teams were drawn together in the last four, UEFA released a statement informing both clubs that any private agreement that had been negotiated regarding the selection of the Belgian stopper was "null, void and unenforceable".
While he refused to directly comment on UEFA's statement, Gourlay has confirmed that Atletico are free to select the 21-year-old over the two-legged tie.
Gourlay told Sky Sports News: "The loan was arranged back in the start of the season. He can play against Chelsea, that's never in doubt.
"Regarding the UEFA statement we'll evaluate that in due course. As far as we are concerned we will comply with loan rules. He can play in both ties against Chelsea if selected. That is fact."
Courtois signed for Chelsea in 2011 but he has spent the past three campaigns in Madrid.