He was diagnosed with a sinus infection and told to let it "run its course", the relative, Peggy Gilbert, told the station.
But after the boy suffered several severe migraines, doctors discovered that the viral infection had spread to the boy's brain, causing blood clots that then led to numerous strokes, according to a GoFundMe page set up by Gilbert.
The teen from Flint, Michigan, died on Sunday, his family said.
"He was my favourite person; now he's not going to be here anymore," his sister, Alexandria Brumley said. "I feel like it's not real. I feel like he's going to come back. But I know he's not going to come back."
Marquel, an eighth-grader, was described by relatives as a straight-A trumpet-playing student who loved football and his family.
"You couldn't find flaws with the kid," his aunt, Nicole Alexander, told People. "He was really helpful. He loved helping people and always had a smile on his face. His daily goal was to make everybody smile."
Alexander said the teen was always telling her "every day without fail, 'love you, Aunt Nicki'."
He was, she added, "really just a sweetheart".
Family members did not say what Marquel's ultimate diagnosis was.
Viral infections, however, can cause encephalitis, a condition where the brain swells. According to the Mayo Clinic, it can cause flu-like symptoms such as fever and headaches, as well as more severe issues such as confusion, paralysis or seizures.
In rare cases, the Mayo Clinic says, the illness can lead to death.
Gilbert wrote on the GoFundMe page last week that Marquel was in critical condition at Mott Children's Hospital in Ann Arbor, Michigan.
"An MRI revealed that the infection was in his brain and had caused blood clots that resulted in multiple strokes," she wrote. "They transferred him to Ann Arbor quickly where he was rushed into surgery. At this time he is in a coma and the doctors are doing everything they can to reduce the pressure in his brain."
Days later, she posted a tragic bulletin on the crowdfunding page: "It is with a very heavy heart that I make this update. Marquel went home to be with the Lord this morning."
Marquel's sister's posted a photo of him on Sunday, saying he had "loved and fought very hard".
"I love you so much Marquel," she wrote. "Heaven gained an angel that loved and fought very hard. Save a spot up there for me. I love you with all my heart. I'm so sorry Marquel."
As of Friday, more than US$15,000 had been raised on GoFundMe to help cover Marquel's medical bills and funeral.
"The love and support everyone has shown is overwhelming and so appreciated," Gilbert wrote on the GoFundMe page. "Marquel was a very kind and loving person that will be missed terribly. The family is taking comfort in know he saved 7 lives with the gift of his organs."
Speaking to People, Alexander, the aunt, added: "It's bittersweet, the human part of us is selfish and would rather have him here. At the same time, if we can prevent another family from feeling what we're feeling, it's a wonderful thing."