The team reached Serie D in 1999 (fifth tier at that time), but quickly relegated back to Eccellenza Sicily.
Siracusa returned to play Serie D in 2002; since then, the Sicilian team unsuccessfully tried to reach a spot into professional football until 2009, when they dominated the Group I of Serie D, getting finally promoted back to Lega Pro Seconda Divisione (ex-Serie C2) in advance of six weeks, after a 2–0 home win to Rosarno in front of 5,000 local supporters.
[6] After the promotion the club dropped the word "amateur" (Italian: dilettanti) from the denomination, to become Unione Sportiva Siracusa S.r.l..
However, due to financial troubles again, instead of being directly promoted to Serie B, U.S. Siracusa was inflicted a penalty of 5 points in the same season, which caused the relegation of the club to a final third position.
[7][8] However, U.S. Siracusa's youth teams were still allowed to play in 2012–13 season, as well as retaining the registration number of the club: 79957.
[10] In the next season the Allievi team finished as the 11th of Group E. However, 2 positions higher than the illegitimate heir, Sport Club Siracusa.
[11] On 31 August 2012, an illegitimate phoenix club was restarted from Terza Categoria – Syracuse Province as A.S.D.