Detectives began investigating reports of corporate bank fraud in 2015.
A Rockdale bank reported the suspicious loss of more than $31,000 to police in 2016.
After an internal investigation by the bank, a 25-year-old man was fired.
Officers arrested the man, now aged 32, in Peakhurst about 6.30am yesterday.
He was taken to Kogarah Police Station where he was charged with several fraudulent offences.
Police will allege the man, who was an employee at the bank, fraudulently obtained the money through separate transactions between October and November 2015.
The man was granted bail and will appear before the court in January.
Investigations are continuing.