Thompson arrives from Arsenal, while Boothe and Healy-Matthews join from Leicester City and West Ham United respectively. All three 16-year-olds will link up with Chris Moore's Under-18 squad as first-year scholars.
Thompson, capped at Under-17 level for England, moved to Arsenal from West Ham as a schoolboy ahead of the 2024-25 season and made his Under-18 debut later that campaign aged 15. He progressed to Premier League 2 football with Arsenal's Under-21 side last season and featured three times in the Under-19s' UEFA Youth League campaign, scoring in a 4-2 win over Bayern Munich.
Boothe rose through Leicester City's academy, making his debut for the Foxes' Under-18 side at 15 before earning his Under-21 bow against senior opposition in the National League Cup last August and adding further Premier League 2 appearances later in the campaign.
Healy-Matthews made six appearances in the Under-18 Premier League for West Ham last season and played a key role as the Hammers won the Under-17 Premier League Cup.
Newcastle United's Under-18 side finished third in the Premier League last term, behind only Manchester City and Manchester United, and the club has continued to recruit aggressively at academy level throughout the summer.
The pathway to Eddie Howe's first team has been well trodden in recent years, with academy graduate Lewis Miley establishing himself as a regular in midfield since breaking through as a teenager, and his younger brother Mason following a similar route after signing his first professional contract this summer.
Academy director Steve Harper welcomed the trio, saying: "We're really pleased to welcome Kyran, Christian and Kyle into the Academy and begin working with them.
"They are exciting players with real potential but just as importantly, they're all hungry to keep improving. It speaks volumes about the environment we're building here that they see Newcastle United as the right place to take the next step in their journey.
"Moving to a new club at 16 is a big step for any young player and we'll make sure they have the support around them to settle quickly and continue developing in the right way."