The 2005–06 season brought the club considerable European success and recognition, due to their consistent performances in the Champions League.
In the qualifying round stage, Villarreal controversially defeated English side Everton with a 4–2 aggregate score with two 2–1 victories.
During that game, left-back Rodolfo Arruabarrena turned a back header from Juan Román Riquelme free kick past Inter goalkeeper Francesco Toldo to score the decisive goal of the tie.
A first win was sealed on 30 September by beating Gordon Strachan's Celtic 1–0 at El Madrigal, courtesy of a Marcos Senna free-kick.
Theo Walcott, Emmanuel Adebayor and Robin van Persie secured a 3–0 win for Arsenal on the return, knocking Villarreal out of the tournament.
For the 2009–10 season, Villarreal competed in the Europa League, defeating NAC Breda of the Netherlands by a 2–9 aggregate victory in a qualifier.
After beating Napoli, Bayer Leverkusen and Twente in the knockout phases, Villarreal qualified for the semi-finals to face tournament favourites Porto.
Having missed Europe during the 2019–20 season after finishing 14th in La Liga, Villarreal played their first European match of the decade on 22 October 2020, beating Sivasspor 5–3 at home in the Europa League.
Villarreal then played Bayern Munich in the quarter-finals, and knocked them out as well after winning 1–0 at home and drawing 1–1 away, reaching their best record in the competition, the semi-finals, as they did in the 2005–06 season.