FC Andorra was founded on 15 October 1942 in Andorra la Vella, the capital of the small Pyrenean principality of Andorra, making it the first football club established in that country. Because Andorra had no domestic football league until 1995, the club crossed the border and joined the Spanish football pyramid as early as 1948, affiliating with the Catalan Football Federation in 1963 and competing in Catalan regional divisions from the 1963–64 season onward.
For much of the club's history, FC Andorra moved between the lower tiers of Spanish regional football. A memorable highlight came in the 1993–94 Copa Catalunya, when the club defeated both FC Barcelona and RCD Espanyol to claim the tournament title — a result that illustrated how a small club, with the right preparation, could upset giants of Spanish football. A Copa del Rey run to the round of 16 in 1995–96 further demonstrated the club's capacity to compete above its station.
The modern era of FC Andorra began in December 2018, when Spanish football icon Gerard Piqué acquired a 90% controlling stake through his company Kosmos Global Holding, becoming club president. Investment and ambition followed quickly: in 2019 the club secured a place in the Segunda División B, and by 2021–22 had won the Primera División RFEF Group B title to earn promotion to the Segunda División — the second tier of Spanish football — for the first time in club history.
Playing home matches at the Estadi Nacional in Andorra la Vella, the club's identity is defined by its unique cross-border status: a team rooted in a sovereign microstate yet competing entirely within the Spanish football system.