The Tottenham boss seemingly opened fire at the Portuguese midfielder and United’s habit of winning spot-kicks last season.
Mourinho said: "Bruno came in, was fit, played very well, improved the United team and also proved to be a great penalty taker, one of the best in the world, because he had about 20 to score."
While the Red Devils set a new Premier League record last season after being awarded 14 penalties in the league 38 games, and won a further eight in cup competitions, Fernandes did not seem too bothered by the comments.
"I honestly did not feel stung," Fernandes told A Bola.
"I feel that I am a good penalty taker and nothing more, I understand, but what I take from his [Mourinho's] words, because I’m a very positive person, is that he said I hit penalties well.
"It is a reality, not least since I arrived at Manchester United."
Fernandes, who moved to Old Trafford in January from Sporting Lisbon, also defended criticism about his strike rate since arriving, with eight of his 12 penalties coming from the spot.
And he pointed to Kevin de Bruyne for his own numbers, claiming only the Belgian has a better goal involvement in England than himself.
He said: “I hear people saying, ah, he only scores from penalty kicks… but a little while ago, I saw the statistics and, except for penalties, only Kevin De Bruyne has a higher involvement in goals than me in England when it comes to midfielders."
Whatever the criticism, there is no doubt that Fernandes’ arrival coincided with a massive upturn in form at Old Trafford.
Ole Gunnar Solskjaer’s men did not lose a game in the Premier League after he joined and they managed to finish in third spot, hence qualifying for the Champions League.
United legend Gary Neville does not think it was a honeymoon period and has backed Fernandes to pick up where he left off next season.
Neville told Sky Sports : "His attitude doesn't tell me, and when you watch him, his performances don't tell me that there's going to be a dip because he just looks like he's got that belief in himself and the courage to take the ball.
"Even if he has a difficult start to the season he'll not lose that belief to get on the ball and go and find space, try and play the pass that is difficult and try and play the ball forward.
"That's the big thing for me, he always looks for a pass forward to try and unlock a team. He's enabled the front three to become a lot better."