The club currently 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 Brentwood Town Youth section was formed in 1996 when an Under 18 side was entered into the Eastern Junior Alliance for the 1996/97 season. The following year an Under 16 team was introduced and they were runners-up in the Eastern Junior Alliance League Challenge Cup in their first season.
The club won the Eastern Alliance Hospitality award for both Under 16s and Under 18s in 1997/98 but the first trophy on the field of play came in 2003/04 when the Under 16s lifted the League Cup by beating Ford United 3-0 in the final at Witham Town. 
When floodlights were installed at the Brentwood Centre in 1999 the Under 18s were able to enter both the FA Youth Cup and the Eastern Junior Cup for the first time, and they have had some good runs in both competitions. 

During the 2004/05 season the Under 18s results have gradually improved, culminating in a run of ten wins in their last eleven matches. They have done particularly well in cup competitions, reaching the semi-finals of the Eastern Junior Alliance Ingilby Cup, and the final of the Magnus Cup in which they defeated Southend Manor 2-0 to lift the first trophy ever won by a Brentwood Under 18 side. They then won the Eastern Junior Cup Plate competition in the same season, defeating Histon 2-1 in the final.  

The Under 16 squad pictured before the Essex County Cup Final 2001 at Purfleet F.C. 

Back row: Brian Hallett (Manager), John Coates, Terry Prati, Daniel Massett, Mark McGregor, Iain Smith, Peter Harlow, Dan Brown, Jamie Kingsley, Pat Davey, Tim Stittle (Assistant Manager), Tom Reilly (Physio)

Front Row: Lee Cable, Kirk Duffield, Jack Harrison, Ricky Holmes, James Reilly, Simon Cockerill, Jordan Marsh, Frank Everett, Jon Moody