The man did not enter a plea and was granted interim name suppression.
The summary of facts was also suppressed.
The man has been remanded in custody until his next appearance on July 2 at the High Court in Hamilton.
Mustafa Ali was taken unconscious to Te Kūiti Hospital on the afternoon of Saturday, June 8, but could not be revived.
Family and friends buried Mustafa at the Te Kūiti Cemetery on Thursday. They gathered around the tiny grave, where a cross, flowers and soft toys were laid.
Detective Inspector Graham Pitkethley said the boy died of violent blunt-force trauma, and the police knew him from non-accidental injuries he received in October last year.
When announcing the arrest on Friday afternoon, he said further charges might be laid as inquiries continued.
Police said Te Kūiti residents could continue to see officers in the area as the investigation continued.
