The 16-year-old is the latest youngster from the Cobblers youth-team set-up to make the jump to the Premier League, following Mark Randall and Anton Blackwood.
"Courtney has been at the club for a number of years and has improved immeasurably in that time," said Town's head of youth Geoff Harrop.
"He's an attacking player, very athletic and has an excellent attitude. He has worked hard, listened well and he, just like Mark and Anton before him, is proof that local players are in good hands here at Northampton Town."
The Cobblers have secured the services of Yas Hussain, another player who was attracting Premier League interest, on a long-term contract.