At around 12pm a man entered the store and threatened two staff members.
He stole cash and medications and ran off towards Featherston Street.
The man was described as wearing a dark green jacket with a hood, grey shoes, black pants and a black scarf partially covering his face.
He was also carrying two yellow shopping bags.
The staff members were not injured, nor were two members of the public who were in the store at the time.
They have been spoken to by Police and been offered Victim Support.
The footpath is cordoned off in front of the pharmacy and a scene examination is underway.
Police are actively searching for the man in the central city area.
Anyone who witnessed the incident or has seen someone matching that description in the central city is urged to contact 111 immediately.
Information can also be provided anonymously via Crimestoppers on 0800 555 111.