Jefferson Lewis, 47, will remain in custody in Darwin but is due to appear in Alice Springs Local Court by video link on Tuesday.
He has been charged with the murder of Kumanjayi Little Baby and other serious offences.
The alleged killing has horrified the tight‑knit community, which spent anxious days scouring creek beds and scrub for the missing girl before her body was found in bushland outside the town five days after she disappeared.
Kumanjayi – the name used in line with cultural tradition after her death – vanished from a home in an Indigenous town camp, triggering a massive land and air search across central Australia.
Lewis was arrested at another Alice Springs town camp after being beaten unconscious by locals.
He was placed under guard at Alice Springs Hospital, where a large, angry crowd gathered demanding he face traditional justice, before Lewis was evacuated to Darwin by the NT Police air wing for his own protection.
The alleged murder gained nationwide attention and fuelled days of tension, including looting and attacks on emergency services.
Five emergency workers were injured, police vehicles and ambulances were damaged and local businesses were ransacked.
More than a dozen people have since been arrested over the unrest, while police are also searching for people who they believe sheltered Lewis during the days‑long search.
Kumanjayi's grandfather, senior Warlpiri elder Robin Japanangka Granites, said the family was relieved Lewis would face court over the death of their "little queen" but begged politicians to respect their "sorry time", a period of deep cultural mourning.
The case has reignited debate over conditions in town camps and the safety of Aboriginal children with opposition calls for inquiries while Prime Minister Anthony Albanese points to billions of dollars in federal spending on remote housing.
Candlelight vigils for Kumanjayi are planned for Thursday and mourners have been asked to wear pink, her favourite colour, as the community comes together to grieve and remember her short life.
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