Assisted by NSW Department of Education officials, detectives established Strike Force Millard last month to investigate reports the girl had been assaulted by a man between 2009 and 2012.
They attended a home in Wiley Park and arrested the accused man just before 10.30 a.m. on Friday.
A search warrant was executed at the home and electronic devices were seized for forensic examination.
The man has been charged with 20 offences including seven counts of aggravated sexual assault, inciting a person under 16 years to commit an act of indecency, procuring a child under 14 years for unlawful sexual activity, and inflicting actual bodily harm.
Police will allege the man sexually assaulted the girl on multiple occasions while she was a student at a school in Sydney’s CBD between October 2009 and December 2012.
He has been refused bail to appear at Parramatta Bail Court on Saturday.