1996/97 saw the launch of an Under-18 side and the club now runs six youth teams from the U13 age group through to U18 in the Eastern Junior Alliance. For 2015/16 season the youth section has amalgamated with Doddinghurst Olympic FC and there are now teams from the under-7 age group upwards representing the club. There are also three Under-21 teams playing in the Ryman League, Essex and Herts Border Combination and Brentwood Sunday League as well as an Under-19 Academy team based at Shenfield School but playing their home games at the Brentwood Arena and competing in the Football Conference Youth Alliance. This Under-19 side had a highly successful season in 2014/15, winning their league as well as reaching the league cup final where they beat Gateshead at Notts County FC.
The club’s youth teams have been particularly successful in cups and over the years the Under-18 teams have featured in many cup finals in the Eastern Junior Alliance and other competitions. In 2014 the Under-18s reached the final of the Essex County Cup for the third season running. On each occasion they had very close matches with the same opponents, Thurock FC, with Brentwood winning the cup in 2012 and narrowly missing out in 2013 and 2014.
The FA Youth Cup was first entered after the installation of floodlights at the Brentwood Arena in 1999 and there have been some good runs in that competition over the years. In 2013/14 the team reached the first round proper but the best performance in the FA Youth Cup was in 2012/13 when the Under-18s reached the second round proper by beating Football League club Gillingham 2-0 at the Arena. They then lost a thrilling match 3-2 to a last minute goal by Brentford at Griffin Park. Some of that Brentwood team were in the club first team squad in the 2014/15 season, which included ten players that have progressed through the youth ranks.