The club was founded on November 16, 1909 as EVV Eindhoven. In 1954, Eindhoven were the last Dutch league champions before the introduction of the professional league. After turning professional in 1954, the club played in the Eredivisie until 1957, when Eindhoven were relegated to the Eerste Divisie, where it would remain until 1969. Two years later, the club secured promotion back to the Eerste Divisie, and in 1975, Eindhoven were promoted to the Eredivisie. In 1977, Eindhoven were relegated back to the Eerste Divisie, where it have remained ever since.
FC Eindhoven's biggest rivalry is with neighbours PSV Eindhoven, against whom they contest the Lichtstad Derby ('City of Light Derby'). Like football rivalries in some other cities, such as Glasgow, the rivalry between Eindhoven and PSV has its origins in religion. Having always been a Roman Catholic stronghold, FC Eindhoven used to be a bigger club than PSV in the period between 1930 and 1955. PSV on the other hand, were of a more Protestant background, being connected with the Philips company.
In 2004, FC Eindhoven contracted a co-operation deal with neighbours PSV Eindhoven, meaning the possibility of swapping youth players between the two clubs, that co-operation ended in 2005