The side consists mainly of Charlton's Academy players who are aiming to break into the first team squad and in the near future. Senior players may occasionally play when returning from injury. The current Senior professional development Coach (U21) at Charlton is Nathan Jones.
In 1999 the team joined the FA Premier Reserve League Southern. Led by reserve-team coach Glynn Snodin had relative success in their first season, finishing 2nd, however in comparison the next 3 seasons were disappointing as the club finished 8th, 7th & 7th respectively. After this however things picked up, and Charlton became unexpected winners of the league in 2003/2004, and this was then followed by a second success at the Charlton team won the division again in 2004/2005, just a season later. This was followed by another good season, seeing the Addicks finish fourth, however popular reserve-team coach Snodin left to join Southampton as first-team coach. Snodin was replaced by Mark Robson for the remainder, however this was short lived as Charlton faced a managerial re-shuffle after the resignation of Alan Curbishley, Mervyn Day & Keith Peacock.
With the installation of Iain Dowie as head-coach, Robson was moved to development coach, working with both the Reserve & First Team sides, however after Dowie was fired he was named assistant head-coach, under Les Reed. Mark Kinsella replaced Robson as development coach until this hiring of current club manager Alan Pardew when Kinsella was moved to reserve-team coach. Despite a hectic season the team still managed to finish 6th, however due to the relegation of the first-team the club were demoted to the Football Combination Central where after spending much of the season top of the table were pipped to the post by Southampton F.C. Reserves on the last game of the season.
In 2008 Mark Kinsella moved to a more senior role within the first team under Caretaker manager Phil Parkinson while the club sought after a replacement for Alan Pardew, who parted company with the club November 22, 2008. He was replaced by the clubs U18 Youth Coach, Damian Matthew, for the interim period. When Parkinson assumed the role of first team manager Matthew was designated Development coach, based on the same role Mark Robson had held previously.
In 2009 the team was disbanded as a competitive side. With the relegation of the first team from the Football League Championship to the Football League One it was decided that the team would no longer play in the Football Combination and instead only played a number of friendly matches throughout the season.
In the last 9 years the reserves have had many different stadia. In their first season they played their matches at Welling United's ground, Park View Road, but the stay was short lived. For the 2000/2001 season the reserve team played their matches at the first-teams ground, The Valley, however when there was a clash in matches the reserve teams would play their games at Park View Road. This system continued until the 2006/2007 when the team moved their matches to Gravesend & Northfleet's ground, Stonebridge Road. The reserve team continued to play their games there in the 2007/2008 season, after the change of club name from Gravesend & Northfleet F.C. to Ebbsfleet United F.C.