The 19-year-old has officially been a free agent since the start of the month but has been training with Albion in that time.
He has now put pen to paper on a new deal committing him to the club until 2022.
It is a boost for the Baggies, who could have lost the teenager for a low compensation fee had he moved across the border to Celtic.
But new boss Slaven Bilic sat down with Harper on the first day of pre-season training and helped convince him to stay.
The England under-19 international is expected to feature prominently in the first team next season.
Technical Director, Luke Dowling, said: “We are pleased Rekeem has committed his future to the club having been with us from such a young age.
“Rekeem is progressing as a player and we are confident that if he continues to work hard he will play a prominent role in the first team over the coming years.”
Harper, who has been at the club since he was 11, was handed his debut by Tony Pulis but enjoyed a breakout season under Darren Moore.
The youngster from Aston became a regular first team player during the second half of last season, netting his first goal in a 2-1 win over Rotherham United in April
Signing his deal this week puts an end to long saga that started back in January when the Baggies first started talks with Harper and his representatives.
He was offered a four-year contract at the end of the season but that has been negotiated to a three-year deal.