It follows the arrest of a Lebanese national - the "husband" - last week on child sex offences.
Police said the imam, reportedly Pakistan-born, was arrested in Sydney on Monday afternoon by the Child Abuse Squad and charged with solemnisation of a marriage by an unauthorised person.
He was granted strict conditional bail to appear in court on 2 April.
Last week police revealed that the Lebanese man, in Australia on a student visa, met a 12-year-old girl in the Hunter region north of Sydney in 2013 and allegedly became involved in a sexual relationship with her.
The pair then allegedly moved to Sydney where they continued the relationship, with police claiming the man and child were married in an Islamic ceremony earlier this year.
While child marriages remain prevalent in parts of the world, in Australia 18 is the minimum age to tie the knot.
The "husband" has been charged with 25 counts of sexual intercourse with a child between 10 and 14 years and remains in custody.
Police have not laid charges against the parents of the girl, but investigations are continuing, police said.