Sebastian Flores began his young soccer career at C.A. Peñarol, a club known for its long time history and success in Uruguay. He later went on to incorporate himself in C.A. Bella Vista, team that had been regulated to the First Division of the Uruguay League, it was a that point in which he declared himslef as a professional soccer player in 2002. Three years later he would achieve the "Apertura" championship of the Second Division on June of 2005 as well as the Uruguayan Championship which allowed the team to be promoted back into the First Division.
As a result of the fantastic campaign, Sebastian Flores would be transfered to Salernitana Calcio, of the Italian League.
He would later on sign for the Aris Thessaloniki F.C. , a club in which he would also obtain the promotion to the First Division of the Greek national league, which later also classified to the presitgiuos UEFA Cup. After going throught the Greek League, Sebastian would signed with CD Cobena which reached the Second Division of the Spanish soccer league.
Sebastian Flores would finally sign with Club Cherno More Varna, which competes in the competive First Division of the Bulgarian Soccer League. In June of 2009, Sebastian assisted the club in their classification towards the UEFA Cup as well as achieving the Bronze title of the Bulgarian League. After grate season with Cherno More, he sign with Botev Plovdiv, famous team in First Division of the Bulgarian Soccer League.
In 2011 and after a long passage through the European football, returns to Uruguay to play in the CA Rentistas team from first division of Uruguay. In September 2012 and after finish contract with CA Rentistas, he signing with CA Torque professional football team from Uruguay, intentions team in its first year as a professional, search a promotion to first division. They loss by penalty definition the final for promotion. After good season with four scores, the capitan of CA Torque singed a contract with Huracan FC.