The Portugal international, top scorer in the competition this season with 12 goals, returned to training with his team-mates on Monday after sitting out Saturday's 2-1 La Liga victory over Atletico Madrid.
He had damaged a thigh muscle as Real lost 4-1 in the first leg in Dortmund last Wednesday.
Even with a fit Ronaldo, Real face a stiff task against the Bundesliga side if they are to keep alive their bid for the 10th European crown that has eluded them since 2002.
"Cristiano is fine to play," Mourinho said.
Aside from injured full-backs Alvaro Arbeloa and Marcelo, Mourinho will be selecting from a full-strength Madrid squad.
Real will be wary of launching a cavalry charge at a Dortmund side unbeaten on their travels in Europe this year as it would leave their shaky defence even more exposed than usual.
They have the leakiest backline of the four teams remaining with 18 goals conceded, and have kept only one clean sheet in the competition so far.
The second leg is also a challenge to Real coach Mourinho's prestige as failure to progress from a third successive Champions League semi-final would test the patience of club president Florentino Perez.
With the La Liga title about to fall to Barcelona, and Real's European campaign hanging by a thread, next month's King's Cup final might end up representing Mourinho's last chance for major silverware this season.
Dortmund look set to recall all their big names for the Bernabeu clash after coach Jurgen Klopp made 10 changes to the team for Saturday's 2-1 Bundesliga win over Fortuna Duesseldorf 2-1 to tighten their hold on second spot.
Klopp will have a full squad to choose from with midfielder Nuri Sahin's Saturday showing, which included the first goal, possibly earning him a starting spot against the team he joined from Dortmund in 2011.
Dortmund, who last week made sure of a Champions League group spot for next season, are looking to reach their first final since winning the trophy in 1997.