The 20-year-old has made twenty-two appearances for The Shots since joining on loan in August 2017 and was voted the club's player of the month for December.
Fowler, who can play either at centre-back or in central midfield, made his senior debut in Ipswich’s Carabao Cup tie against Crystal Palace last year, having signed his first professional contract in April 2016.
Born in Chelmsford, Fowler had featured for Town’s under-21 side aged just 15.
Fowler is the second player to commit to The Shots for next season, after fellow Ipswich Town academy graduate Adam McDonnell signed an eighteen-month contract last week.