The 36-year-old from the rural town of Scottsdale was arrested on Thursday, following a large-scale search of nearby Nabowla a day earlier.
He was detained in custody and is expected to appear in Launceston Magistrates Court on Friday.
Tasmania Police earlier confirmed remains found on a bush track at Nabowla were human and likely belonged to Shyanne-Lee, who was last seen in Launceston on the night of April 30.
Northern district commander Kate Chambers said her heart was with the community.
"We will not rest until we have answers. This latest development is hopefully another step toward having those answers," she said.
"Our investigators and all those involved in this process so far have worked tirelessly to try and find closure for Shyanne-Lee's family and her loved ones.
"We will continue those efforts until we are satisfied we have provided that closure."
Forensic testing on the remains could take one week.
Commander Chambers said a number of items had been seized during searches over the past two months.
Police searched a property at Scottsdale after declaring it a crime scene and have previously said a "specific line" of inquiry was being followed.
The search at Nabowla involved 180 people, including helicopter crews and search-and-rescue volunteers on horseback.
Shyanne-Lee was last sighted on CCTV near the North Esk River in Launceston, about 50km southwest of Nabowla.
Thorough searches of the river area failed to uncover any trace of the teenager, who had been staying in youth accommodation for the two weeks before her disappearance.
She was on her way to visit a friend at nearby Ravenswood when she went missing.
More than 100 people, including members of Shyanne-Lee's family, held a vigil in June.
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