The 34-year-old Frenchman joined Rayo on loan from Deportivo Alavés ahead of the 2022-23 campaign before completing a permanent transfer a year later.
He has since become one of the most important figures at the club, making 157 official appearances and scoring 11 goals.
This season Lejeune has been Rayo's most-used outfield player, accumulating 4,328 minutes across all competitions and missing only one match — through suspension — throughout the campaign.
His performances have been central to a historic run that includes a Conference League semi-final against Strasbourg this week, the most significant European adventure in the club's 102-year history.
The renewal extends a partnership that Rayo had made clear they wanted to preserve.
"From his arrival at the club in the 2022-23 campaign, Florian has been a key player in the first team's successes. We are very happy to continue our journey together," the club announced.
Lejeune began his career in France before moving to Villarreal, then Girona, before becoming a recognisable figure in English football with Newcastle United. He joined Alavés in 2020 and eventually found his most settled period at Vallecas.