England lost to Switzerland and Portugal in the group stages while victory over Croatia in their final game counted for nothing.
Boothroyd had been in charge of the England u-21’s since 2016 when he replaced Gareth Southgate and led them to win the 2018 Toulon tournament.
“It's been the greatest privilege to represent the FA and lead England teams into high-profile tournaments,” the 50-year-old told the FA’s official website.
"While we didn’t finish in the way we wanted, I'm very proud to have been able to work so closely with players who I know will go on to have remarkable international careers and to have experienced some very special moments with them over the years.
"I'd like to thank my staff and all of the incredible support team that have done so much to help us remain competitive against other elite nations. In every single get-together they embraced our unique challenge of rightly prioritising the needs of the senior team while ensuring we gave our all to try and get a positive performance and result."
Three Lions manager Southgate paid tribute to Boothroyd following the announcement after he helped players like Mason Mount, Jude Bellingham and Phil Foden make the step up to the senior squad.
"I’d like to thank Aidy for his wholehearted support and dedication to developing English players and coaches across the last seven years,” Southgate said.
"His pride in working with all of our development teams has shone through and his support of the senior team has been greatly appreciated. I wish him every success on the next step of his career.”
