Detective Senior Sergeant Nik Leigh, Dunedin CIB, said the youth had been charged with burglary and unlawful taking in relation to the December 4 incident.
Michael Hill Jeweller and Sunglass Hut were both targeted in the theft, the latter of which had the glass on its display cabinets smashed and an unknown number of items stolen.
Sergeant Matt Lee, of Dunedin, said police were alerted by a security guard at 4am, after a glass break alarm was activated at the Meridian Mall.
"CCTV footage has confirmed three offenders have damaged a door at the Hanover St entrance and entered the mall."
Police are continuing to investigate a ram-raid at Golden Centre Mall this week and other similar recent offending, and are following positive lines of inquiry, Det Snr Sgt Leigh said.