Local media reported doctors made an eleventh-hour decision not to transfer the boy to a bigger hospital with a paediatric emergency unit in Porto, the nation's second biggest city, because of the severity of his condition, according to the Mirror.
Vitor's death comes just three days after a 16-year-old schoolgirl succumbed to the disease in Paris.
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Tributes have started pouring in for the teen, who was a talented futsal player, an indoor football game popular in Portugal and Spain.
"This time you didn't get past the rival, like you did so many times," Vitor's futsal club at the Aveiro Football Association Maceda Cultural and Recreational Centre said in a statement.
Futsal coach João Jorge posted an emotional Facebook post and warned young people to stay at home.
"Today we are sadder to see a young man from the Futsal family," he wrote. "We are sad, very sad, but your case makes us even more alert. Young people, stay at home for you and all.
"I feel for the family and club mates. May you rest in peace."
Portuguese Football Federation chief Fernando Gomes also paid his respects, calling the youngster a "precocious talent".
At just 14, Portuguese schoolboy Vitor Godinho is believed to be Europe's youngest coronavirus fatality so far. Photo / Facebook
"With profound consternation I am sending my condolences to the family, friends and colleagues of Vitor Rafael Bastos Godinho," Gomes said.
"At this moment of deep pain for his loved ones, I am also sending words of comfort to the footballing family in the Aveiro region who share with us the disappearance of such a precocious talent."
French schoolgirl Julie Alliot, 16, was previously described as Europe's youngest fatality after she died in a Paris on Friday. Her family said she too had no underlying medical conditions and fell ill soon after developing a cough.
