Shackleton has committed his future at Elland Road, agreeing a four-year deal, running until the summer of 2024.
The midfielder first joined Leeds United at the age of seven, progressing through the Academy to the first-team setup.
He made his senior debut under Marcelo Bielsa in the 4-1 victory over Derby County in August 2018, before making his first start three days later in the Carabao Cup against Bolton Wanderers at Elland Road.
Last season, Leeds born Shackleton helped his boyhood club become Sky Bet Championship champions, making 22 appearances for the Whites, who clinched the title by 10 points.
He scored his first goal for Leeds at Pride Park in July and followed that up with his first goal at Elland Road against Charlton Athletic in the final match of the season.
The 20-year-old has made a total of 48 appearances for Leeds in all competitions and becomes the latest young player to commit his future to the club.