Ashton Chungaloo, 26, was charged days after the girl died at Alpurrurulam, near the Northern Territory-Queensland border, about 1500km from Darwin.
He allegedly assaulted the girl before she arrived at the Alpurrurulam health clinic early on Monday.
The teen suffered cardiac arrest upon her arrival at the clinic and later died, police said.
"It was at that time that the clinic staff also noticed that she had (a) number of injuries to her body," Acting Commander Mark Grieve told reporters in Darwin on Monday.
Chungaloo was believed to have been in a "domestic relationship" with the girl, police said.
He was arrested on Monday and transferred to Darwin as detectives and forensics officers travelled to the remote community to investigate the death.
In Darwin Local Court on Thursday Judge Steven Ledek remanded Chungaloo in custody to appear in Alice Springs Local Court on December 10.
Police believe the girl was transient but primarily resided in Queensland near Mount Isa, about a four-hour drive from Alpurrurulam.
Alpurrurulam has been the scene of recent community unrest, prompting the evacuation of its health clinic staff.
However, Mr Grieve said police believed the teen's death was unrelated to the unrest.
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