Fernandez, 13, was tried as an adult but will be sentenced as a juvenile under a plea agreement, court officials said.
He will likely be released from the Department of Juvenile Justice on his 19th birthday if he adheres to the conditions of the plea agreement, The (Jackonsville) Times-Union said.
He will also serve eight years of probation and will need to stay away from his siblings, court officials said.
But if he violates probation, he will be sentenced for his crimes as an adult, The Times-Union said.
Fernandez was initially charged with first-degree murder at the age of 12, The Times-Union said.
He allegedly slammed his half brother David Galarraga head into a bookshelf in their apartment in March of 2011.
Fernandez's mother, Biannela Susana, pleaded guilty last year to aggravated manslaughter after admitting waiting eight hours to take David to the hospital, The Times-Union said.
Susana faces 30 years in prison when sentenced.