The 28-year-old midfielder joined the Spanish club from Tottenham in 2012 and worked under Mourinho for a season before the Portuguese left for Chelsea.
Reports have suggested that the pair could be reunited at Stamford Bridge this summer but Mourinho claims Modric will remain at Madrid.
"I called Modric only privately but he doesn't want [to join] Chelsea,” Mourinho told Croatian newspaper Sportske Novosti.
"You know I really appreciate Luka Modric and his qualities. But he stays in Real Madrid.”
Modric made 49 appearances in all competitions for Madrid last season, scoring two goals and providing eight assists, while Manchester United have also been linked with a bid for the 28-year-old.