The 36-year-old stumbled in the bullring after catching his feet in his cloak and was gored by the bull, whose horn punctured his lung.
The Basque fighter was performing at the Aire-sur-l'Adour bullfighting festival in France with fellow matadors Juan Del Alamo and Thomas Dufau.
Fandiño had won an earlier fight and cut off the bull's ear. He was photographed being carried away from the scene by his colleagues with blood seeping through his embroidered traditional costume.
Hospital authorities declined to comment but an independent medical source told AFP that Fandiño had suffered two heart attacks in the ambulance and died later in hospital in the nearby town of Mont-de-Marsan.
Fandiño is assisted after being impaled by the bull. Photo: Iroz Gaizka/AFP
The last time a bullfighter was killed while performing was in July 2016 when Spanish matador Victor Barrio, 29, was gored in the chest live on television. Just over a month earlier, 64-year-old Mexican fighter El Pana died after weeks in hospital, having also been gored in the chest.
Hailing from Ordonu close to the northern Spanish port city of Bilbao, Fandiño was well known for his daring, never hesitating to fight bulls that his colleagues had declined to take on. In Bilbao in 2012 he single-handedly took on six bulls put forward by six different breeders.
The centuries-old tradition of bullfighting remains popular in Spain, with around 1,800 shows a year before a total audience of some six million "aficionados" who see the sport as an art integral to Spanish culture.
But authorities are under increasing pressure to clamp down on the sport on animal rights grounds.
Activists renewed calls for a total ban after Barrio's death, saying the tradition is both cruel and anachronistic, while a year ago the regional government of Castilla y Leon banned the killing of bulls at town festivals.
The nationalist regional government of the northern Catalonia region outlawed the practice in 2012, but Spain's Constitutional Court overturned the ban in October 2016.