The history of FC Lisse is linked to its Catholic religion, the first version of a football club being formed in 1911 by a local Catholic priest, called Lissese Voetbal Vereniging, which was later renamed Lisse Racing Club.

In 1942 Lisse RC was dissolved, and after World War Two another club, Lisser Boys, was formed.

The club was automatically promoted to Topklasse in 2009–10, which was introduced as highest amateur level in the Netherlands.

After reintroduction of the Tweede Divisie in 2016–17 above the Topklasse, FC Lisse didn't qualify for the new top amateur championship.

In the 2024–25 KNVB Cup first round, Lisse hosted Eredivisie club FC Utrecht, where they narrowly lost 2–1.