Hunter Boutain became ill after swimming in Lake Minnewaska, in the west-central area of the state. He died Thursday.
"Hunter's condition deteriorated throughout the night and he was declared brain dead (Thursday) morning," the Boutain family said in a statement. "Hunter died surrounded by his family. It is a deeply emotional time for all us."
"I thank you all for praying for Hunter Boutain," his older brother, Lee, wrote on his Facebook page. "The Lord didn't want him to stay on earth. As much as I am hurt I know I can't love him as much as GOD."
The Minnesota Department of Health was investigating Boutain's illness as a suspected primary amebic meningoencephalitis, known as PAM.
It is a very rare, but deadly brain infection caused by the Naegleria fowleri amoeba.
A California woman died from the same infection earlier this month.
But there were only 35 cases in the United States between 2005 and 2014. Since 1952, there have been about 133 known cases. According to the Centers for Disease Control and Prevention, only three people survived.
Someone can get infected with PAM from swimming in warm fresh water, such as a lake or river. The amoeba enters the nose, and then goes to the brain, where it causes swelling that is almost always fatal.
Even though it is rare, people should be aware of the potential risks of swimming in lakes and try to limit how much water goes into one's nose, as that is how the amoeba enters the body.
According to the CDC, symptoms include headache, fever, vomiting, seizures and hallucinations.
It is not contagious.