Emmanuel Deshawn Aranda, 24, was charged with attempted premeditated first-degree murder.
Aranda told police he had come to the mall a day earlier intending to kill an adult, but that did not "work out", according to the complaint.
Prosecutors will ask that bail be set at $2 million.
The child's mother reportedly told authorities that she and her son had been with a friend and her child on the mall's third floor outside the Rain Forest Cafe when a male she had never seen before approached them. He gave his name and address when prompted by Judge Jeannice Reding and answered "not at all" when the judge asked if he had any questions.
Landen Hoffmann plunged nearly 12 metres and is fighting for his life in a Minneapolis hospital with head trauma and multiple broken bones.
Stephen Tillitt, an attorney representing the victim's family, told reporters the child remains in critical condition. Court documents claim Aranda said he originally planned to kill an adult before choosing the child instead. He's been convicted in the past for assaults at the mall, including an incident in 2015 where he tossed a glass of water and a glass of tea at a woman who wouldn't purchase something for him.
When Aranda tried to flee the scene, a witness attempted to stop him from leaving, but Aranda pushed the person against the wall and continued running, according to prosecutors.
After being read his Miranda rights, Arnada confessed that it was he who threw the boy off the balcony.
Police caught Aranda on a light rail train at the mall waiting for it to leave.
"Defendant indicated he had been coming to the Mall for several years and had made efforts to talk to women in the Mall, but had been rejected, and the rejection caused him to lash out and be aggressive", a complaint said. The Star-Tribune reported that Aranda was previously convicted of first-degree property damage and was also arrested on charges of assault and theft in IL.
Police have not identified the boy, but said he suffered life-threatening injuries from the fall at the Bloomington mall, a major tourist attraction in the state.
Paul Sellers, the public defender appointed to represent Aranda, said his client has been in mental health court before.