Virginia had entered the final year of the contract he signed in the summer of 2018 but has now put pen to paper on a deal that will keep him at Goodison until June 2024.
The 20-year-old is in contention to face Fleetwood Town tomorrow night in the third round of the Carabao Cup having made his Everton debut in the previous round against Salford City.
Virginia, a Premier League 2 title winner with Everton in his first season at the club, joined from Arsenal and the club have been keen to tie him down to a new contract for some time.
A season-long loan to Reading was brought to a premature end in January, after the Portuguese youth international, fell down the pecking order with the Championship club, and he has remained as part of the Blues’ first-team set-up ever since.
The summer release of Maarten Stekelenburg means Virginia has earned his shot this season.
Virginia was on the bench eight times last term and has been in the Blues’ Premier League matchday squad on both occasions so far this season.
Jonas Lossl is said to have been ruled out of both games with a back injury.