The 1999–2000 season saw Sydney United embark on its seventeenth season in the National Soccer League (NSL). They finished last, winning the wooden spoon for the first and only time in their NSL history. 
The 1999–2000 season marked a transitional period for the club, as it embarked on a major rebuilding effort. The departure of Dave Mitchell, who had previously guided the team to a premiership and Grand Final appearance, had a profound impact on the club's fortunes. Mitchell's decision to join the newly established Parramatta Power franchise resulted in the loss of 16 key players, who opted to follow him to the new club. Notably, Captain Velimir Kuprešak demonstrated his commitment to Sydney United, remaining the sole player from the previous season's Grand Final squad to stay with the club.
David Ratcliffe was appointed as the new head coach, tasked with rebuilding the team from scratch. However, poor results led to his mid-season sacking, with assistant coach and former player Ivan Petković taking over the reins for the remainder of the season. Unfortunately, the team's struggles continued, and they finished the season with a disappointing last-place finish, managing only 5 wins from 34 games.
Despite the turmoil, Sydney United had been invited to participate in the Shanghai International Football Tournament during the pre-season, courtesy of their premiership win in the 1998–99 National Soccer League. However, despite an admirable effort, they were eliminated in the group stage, failing to advance further in the competition.
Players.
Transfers out.
 
Statistics.
Appearances and goals.
Players with no appearances not included in the list.