Ibrahimovic, 35, arrived from Paris Saint-Germain in July on a one-year deal with an option for a further year, which Mourinho in November indicated United would look to take up.
After the footballer scored once and made two goals in United's 3-1 win over Sunderland on Monday, Mourinho said the clause had not been activated yet, but would be.
“It is activated in his brain and it is activated also in my decisions and in the owners' and the board's. So it is no problem,” said Mourinho.
Ibrahimovic's goal agains Sunderland means that he has scored 50 times across all competitions for club and country during 2016, the year he retired from international football with Sweden.
“I am not really surprised because he is a very intelligent guy and a very proud man,” Mourinho said.
“He decided to come to Manchester United and to the Premier League, to a club with the level of expectation of Manchester United, in the most difficult league in the world for a striker.
“When he decides to come here, it is because he knows he can do it.”
“When we contacted him and he said, yes, he will come, I was sure that he was not coming here to leave the Premier League without proving himself.”
“To leave the Premier League having failed at Manchester United? No way. When such a guy decided to come, I was completely clear that he would be ready and he is ready for more next season. He will be here again,” said Mourinho.
Ibrahimovic set up Daley Blind to put United ahead in the 39th minute and then ran through to score from Paul Pogba's pass before setting up Henrikh Mkhitaryan for a spectacular 'scorpion kick' volley.
United secured a fourth successive Premier League win, and extended their unbeaten record in all competitions to 11 matches.