Kyoto Sanga FC traces its roots to 1922, when the Kyoto Shiko Club was founded in Kyoto — making it the oldest predecessor of any club currently competing in the J.League. Unlike most Japanese clubs of that era, it was built as a dedicated football club rather than an arm of a corporation, a distinction that shaped its independent identity from the start. The name "Shiko" (紫光) means "brilliant purple," a colour with deep resonance in Kyoto: purple is the imperial colour of a city that served as Japan's ancient capital for over a millennium.
The club professionalized in 1993 under the name Kyoto Purple Sanga, backed by local sponsors Kyocera and Nintendo, and joined the J.League in 1996. Its maiden top-flight era was turbulent — Kyoto holds the record as the J.League's most-relegated side, having dropped from J1 to J2 at the end of the 2000, 2003, and 2006 seasons. The 2003 relegation is particularly remembered because the squad at the time included future European stars Park Ji-sung and Daisuke Matsui. Despite those struggles, the club captured the Emperor's Cup in 2002, defeating Kashima Antlers in the final — the first major title won by a Kansai-based club in the J.League era.
The club shortened its name to Kyoto Sanga FC in 2007, reflecting a fresh identity rooted in the Sanskrit word "sangha" — meaning community or fellowship — a nod to Kyoto's heritage as a centre of Buddhist culture. In 2020, the club moved into Sanga Stadium by Kyocera in Kameoka, the first football-specific professional stadium in Kyoto. After an eleven-year absence from the top flight, Kyoto returned to J1 in 2022 and have established themselves there since, achieving their highest-ever league finish of third place in 2025.