The former Ireland senior international has been Head Coach of the WU16s side for five years and has seen a number of players progress from her squad up to the Women's Senior Team.
Current internationals such as Leanne Kiernan, Heather Payne, Amy Boyle-Carr, Isibeal Atkinson and Tyler Toland have all featured for Boyle's side in recent years, thus proving that the U-16s plays an important role in player development.
In May 2016, the WU16s won a UEFA Development Tournament following victories over Hungary, Bosnia & Herzegovina, and Slovakia. Boyle's final game in charge saw Jessica Ziu score the only goal of the game in a 1-0 win over Turkey in Sweden earlier this month.
"I've been involved with the international teams for a number of years now, as a player and then progressing into management," said Boyle.
"It's been an incredible opportunity for me to see so many young players progress and develop their skills and footballing abilities, and it's been an honour to be part of their journey.
"Now, I feel it is the perfect time for me to take a break and I would like to take this opportunity to thank everyone who has supported me over the years, especially my assistant Paul Martyn and my backroom staff. I would also like to thank the FAI for their support over my decision and wish the team the best of luck in the future."
FAI CEO John Delaney thanked Boyle for her dedication to the role and the impact that she made over the course of five years.
"The early stages of development on the elite player pathway are so important and it is a credit to Sharon that so many players who she coached have gone on to forge successful careers at international level and in the Continental Tyres Women's National League," said Delaney.
"Sharon has been an influential figure in the growth of women's football over the past number of years and her work with the Under-16s will form a foundation that the next head coach can build on to help more girls develop as players."
FAI High Performance Director Ruud Dokter said: "I would like to thank Sharon for her all of her hard work in the role over the last few years.
"As you can see from a number of current WNT internationals who've come through her side, Sharon has been crucial in helping us develop talented young footballers as we look to take women's football to a new level in Ireland.
"Sharon's team has consistently performed in the UEFA Development Tournaments and have benefitted hugely from her exceptional experience and coaching, and I'd like to wish Sharon the best of luck in the future."
Boyle will continue in her role as FAI Development Officer, while the WU16 role will be reviewed ahead of a recruitment process.