Nicknamed Ruso, Flores was signed by top Argentine side River Plate and played for River Plate's Reserves team in 2006–2008. He impressed in Argentina, but was unable to stay due to his age. Upon returning to El Salvador he signed with A.D. Isidro Metapán in 2009. During his time with the club Metapán enjoyed the greatest period in its history capturing four domestic titles, the last one in December 2011. On 29 January 2012, Flores signed to first division Danish club Viborg FF. Due to injury he only played one league game, but played several games in the Danish Cup, where he scored two goals. He did not renew his contract with Viborg and went back to El Salvador to play with Metapán.
On 18 July 2014, the New York Cosmos announced that Flores would be signed on loan from Turín FESA F.C.. The 23-year-old made his first appearance for the New York Cosmos on 2 August 2014 in a 1-0 loss against the Carolina RailHawks. On 9 August 2014, Flores scored his first goal for the Cosmos in a 2-1 win over the Atlanta Silverbacks. Flores battled a hamstring injury towards the end of the season and finished the year with one goal and one assist in eight appearances for the Cosmos. Flores also earned NASL Fall Team of the Week honors twice. Flores earned multiple call-ups to the El Salvador national team while with the Cosmos including to Copa Centoramericana and multiple friendly matches. In the 2015 NASL season, Flores started 11 times in 20 appearances, logging 1,044 minutes, while picking up three goals and three assists.
Portland Timbers
In January 2018, Flores signed with Portland Timbers of Major League Soccer.
International career
Flores started playing for the U-15 national team, and has been an essential player in the youth national teams. In 2008, El Salvador's manager Carlos de los Cobos called the young Flores to train with the senior team. He made his debut for El Salvador in a March 2008friendly match against Trinidad & Tobago but was overlooked from May 2008 on, only to be recalled for a September 2010 friendly against Honduras. Flores took part at the 2011 CONCACAF Gold Cup. He was subbed-on at the 78th minute in exchange for Léster Blanco in a friendly on 7 August2011 against Venezuela. Flores was named as the captain of the El Salvador squad for 2014 Copa Centroamericana. Flores started four matches for El Salvador during the tournament and led the team to an overall record of 2-0-2 and a fourth-place finish in the tournament. In August 2018, Flores became a United States citizen.
