The youngster was found to have a tumour in his leg in November 2016, prompting his retirement in order to undergo treatment.
The Portuguese side continued to honour his contract and wages, however, and earlier this month renewed his deal until 2019.
Edu partiu, mas nunca nos vai deixar!— Boavista FC (@boavistaoficial) December 24, 2017
Hoje, há mais uma estrela no Céu 🌟
Descansa em Paz, Edu! pic.twitter.com/Qdstqqv4BJ
In a statement the club confirmed that he had lost his battle against the disease on Christmas Eve.
"Edu has left, but he will never leave us!" it said. "Understanding the match may be something very difficult, especially when the sadness knocks on our door because we just lost one of our own.
"We will dedicate this day to remember the good times that have been shared.
"That the pain of our loss can be reduced every day and that, from now on, this absence will turn into good memories and be able to further strengthen the ties of our family.
"The emptiness that has remained will never be filled in our hearts. Today, there's another star in the sky. Rest in peace, Edu!"
Edu had come through the ranks of Boavista's youth system and worked his way into first-team contention just months before his diagnosis.