The teenager joined the gunners from Benfica three years ago and played for their youth squads up until this summer.
"Goalkeeper Joao Virginia has joined Everton for an undisclosed fee," the Gunners announced via their official website on Friday.
"The 18-year-old signed for us from Benfica in summer 2015 and featured for our under-18s and under-23s.
"We would like to thank Joao for his contribution to the club and wish him well for the future. The transfer is subject to the completion of regulatory processes."
The player has since expressed pleasure having moved to Goodison Park and added that he is hoping to learn from the club's senior stoppers Jordan Pickford and Maarten Stekelenburg.
"I am really happy to be at Everton," the Portuguese starlet told Everton's website.
"I hope to learn a lot from the goalkeepers here, Jordan Pickford, who had a great season and World Cup and Maarten Stekelenburg, who is very experienced, too. This is a great opportunity for me.”