Emmanuel Aranda, 24, is charged with attempted first-degree murder in the April 12 attack.
Police said Aranda told them he went to the mall "looking for someone to kill" and chose the boy at random.
Aranda's bail was kept at US$2 million and an omnibus hearing was set for May 14.
KSTP's Brett Hoffland said the court appearance lasted about five minutes.
About 10:15 a.m. Friday, Aranda was back at the mall, where he allegedly approached the victim and the victim's mother as they stood outside the Rainforest Café on the third floor with another parent and child.
She said she asked him if they were in his way and should move, and he picked up the child without warning and threw him off the balcony, according to the complaint.
"During my most recent visit with Landen, holding his hand revealed a calm and warm aura in his room, one that likely is contributed from all of the vast outpouring of prayer and support from everyone across the globe", Noah Hanneman wrote Monday night on a GoFundMe page collecting donations to help with the family's expenses. The complaint states medical personnel indicated he had multiple fractured bones and severe head trauma.
The boy, who has not been publicly identified, remains in critical condition, his family said in a statement through the Bloomington Police Department. Court documents claim Aranda said he originally planned to kill an adult before choosing the child instead.
According to a criminal complaint, Aranda told investigators after his arrest he was angry over being rejected by women he attempted to talk to at the mall, "and the rejection caused him to lash out and be aggressive". It also states there is a warrant for his arrest from IL for assault.
Surveillance video at the mall shows Aranda walking in the mall on the third floor, looking over the balcony several times, before approaching the victim and his mother, CBS Minnesota reports.
Aranda, who has roots in the Chicago area, has a felony conviction for first-degree property damage as well as a long string of misdemeanor arrests and convictions.
Police caught up with Aranda as he was waiting for a light rail train to depart at the shopping center. 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.