The story of FC RFS begins with a coach who left his club and took his pupils with him. Until 2003 the core of the future side was a group of boys born in 1990 and 1991 who trained in the youth section of Skonto under Vladimirs Beļajevs. That year Beļajevs left with his students and founded the Daugava Football Sports School. Two years later, on 19 May 2005, the senior team FSK Daugava 90 was established. It entered the Latvian First League in 2007, was renamed FK Daugava a year later, won promotion to the Virslīga in 2008 and was relegated in 2009. The club later operated as Rīgas Futbola Skola, which gave it the abbreviation RFS, although it has no connection with the city's youth academy of the same name, founded in 1962.
The turning point came in early 2016, when the Latvian Football Federation revoked the licence of Skonto and awarded it to this club, which re-branded itself as RFS. The pupils thus took the top-flight place of the institution their teacher had once left. The first Virslīga season ended in sixth place. The construction and development group LNK Industries later became the club's owner, and the legal name was changed to FC RFS in May 2023. A third place in 2018 secured the first European qualifiers, and in 2019 RFS won its first trophy, the Latvian Cup, beating FK Jelgava in the final. In 2021 it completed a domestic double, winning its first Virslīga title alongside the cup.
The European record is the club's most distinctive feature. After a debut in the 2019–20 Europa League qualifiers (a 3–4 aggregate loss to Olimpija Ljubljana), RFS entered the Champions League qualifiers for the first time in 2022, lost to HJK Helsinki and dropped into the Conference League. It then eliminated Hibernians and, after a penalty shoot-out, Linfield, becoming the first Latvian club in the group stage of that competition and only the second Latvian side in any UEFA group stage, after Ventspils in 2009–10. In Group A, against Fiorentina, Hearts and İstanbul Başakşehir, RFS finished last. The 2024–25 season brought the league phase of the Europa League, and on 23 January 2025 RFS beat Ajax 1–0 at the Daugava Stadium in Riga, with Adam Marhiev scoring in the 78th minute. It was the first victory by a Latvian club in a UEFA group or league phase match. With home draws against Anderlecht and Galatasaray, the club ended that campaign with five points.
Domestically, RFS and Riga FC have been the two dominant forces since 2016. The titles of 2021, 2023 and 2024 were won in tight races: in 2023 with 89 points to Riga's 88, in 2024 with 90 points to 87. The Latvian Cup followed in 2019, 2021 and 2024, and the Latvian Super Cup in 2025, the year in which Riga FC retook the championship and RFS finished second. In 2022 RFS was named Best Sports Club in Riga. The team plays in blue at home and white away, and its matches are held at the privately funded LNK Sporta Parks. The former Latvian international Māris Verpakovskis has served as general director since 2018, and Viktors Morozs was head coach during the 2024–25 European campaign. RFS has entered UEFA qualifying every season since 2019, most recently in the 2026–27 Conference League, and the Riga derby against Riga FC remains the fixture that defines the Latvian game.