Staff and tourists were evacuated from the landmark as police locked the precinct down and began searches of the area.
Manly ferry wharf was also searched after the threats were made on and ferry services were cancelled between Circular Quay and Manly.
Tourists watched on from the police tape at Circular Quay as police scoured the area for nearly an hour and a half, declaring the area safe at around 3.30pm.
Police said nothing of interest was found during the searches.
The 17-year-old was charged with false representation resulting in police investigation and is due to appear at a children's court next month.
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