Faria, who has worked alongside Mourinho for 17 years and is known to be his closest ally at Old Trafford, is expected to pursue an opportunity as a manager in his own right.
The 42-year-old will take to United’s bench for the final time in next weekend’s FA Cup final against Chelsea.
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“After a lot of consideration, and with a very heavy heart, I have decided the time is right for me to move on,” he told the club’s official website.
“I have had 17 years of incredible and unforgettable experiences. However, I have felt for some time that I would like to spend much more quality time with my family before pursuing any new challenge in my professional life.
“My heartfelt thanks go to the manager, Jose Mourinho, for the belief he had in me, all those years ago, when it all was just a student dream. I would like to thank him for the opportunity and confidence, for the knowledge and experience, but most importantly for his friendship.
“I would also like to thank Manchester United and all the clubs where I have had the privilege of working during this period. I would like to say a big ‘thank you’ to all the staff and players who, in different ways, have made an important contribution to my growth as a person and as a professional.
“I wish you all the best for the future, knowing that you will always be my close friends.”
It is not yet known who Mourinho will choose to replace Faria with or if he will be replaced at all but the Portuguese took the time to thank his “brother” for all of his efforts over the last two decades.
“17 years… in Leiria, Porto, London, Milan, Madrid, London again and Manchester. Training, playing, travelling, studying, laughing and also a few tears of happiness.
“17 years and the kid is now a man. The intelligent student is now a football expert, ready for a successful career as a manager.
“I will miss my friend and that is the hardest thing for me, but his happiness is more important and, of course, I respect his decision, especially because I know that we will always be together. Be happy, brother!”