The 19-year-old midfielder claimed to have a back injury during the Blues' friendly victory over Sydney FC, but Mourinho felt the player was only struggling when the opposition had possession.
The Chelsea boss believes his relationship with Loftus-Cheek has taken "one step back", but Terry feels his team-mate can learn from the incident and kick on when he returns for pre-season.
"He's a young boy and he needs to take it on the chin," he told reporters.
"If you want to get into this team you need to be very good and, secondly, you need to be mentally strong.
"The manager picks his times when he digs people out; that's part of his learning curve and he's got the offseason to think about that now.
"He's made a couple of games, come on a couple of times and started a couple of games late in the season, but for him to make that next step and become a regular, it doesn't happen easily. It's going to be hard work for him.
"We've all been there as players and you look for the people or friends around you, but more importantly it has to come from within him.
"He's a great boy, he's got unbelievable talent and he just needs to kick on now. I'm sure he will, but as captain I'll have a quiet word for sure."