Newtown Synagogue, in Sydney's inner west, was spray-painted with red Nazi swastikas and briefly set alight in the early hours of January 11.
It was one of a series of recent cases in which Jewish facilities and communities were targeted in arson and graffiti attacks, sparking a major police investigation involving state and federal officers.
A 33-year-old man was arrested on Tuesday evening over the Newtown incident and initially taken to hospital before he was transported to a police station and held overnight after being denied bail.
He is expected to face Sydney's Downing Centre local court on Wednesday, charged with two arson and property damage related offences, as well as possessing suspected stolen goods and cultivating a prohibited plant.
NSW Police Commissioner Karen Webb said a second man was expected to be arrested soon in relation to the same incident.
"The arrest this morning is 11 days on from that incident, with very, very little information other than a very hazy CCTV image," she said.
"We've worked backwards from that, tirelessly, methodically and now we have someone before the court and a second offender we are currently searching for."
Australian Federal Police commissioner Reece Kershaw on Tuesday said the force was probing 15 serious attacks since December and was considering whether overseas actors or individuals paid local criminals to carry out some of the crimes.
But Ms Webb would not be drawn on motive in the latest case before the court, saying investigations were ongoing.
"We can't rule anything out anything and we need to keep an open mind, which we are doing," she said.
Following the attack, police released images of two hooded figures they believed may have been involved, one of whom they said was riding a mountain bike and the other a motorised scooter.
The offenders ignited a clear liquid which burned out in minutes, but it could have had deadly consequences if it had taken hold, Ms Webb said at the time.
Strike force detectives raided two properties in Camperdown, not far from the synagogue, seizing a number of items for further examination in the process.
The allegations against the 33-year-old and others charged over separate incidents carried heavy penalties, but the charges could also potentially be upgraded to include terrorism offences, Ms Webb said.
The man is the ninth person charged under Strike Force Pearl, which was formed by NSW Police to investigate a spate of anti-Semitic attacks in recent months.
The number of detectives working full-time on the strike force has been increased to 40.
Premier Chris Minns labelled the latest arrest a "big breakthrough", adding hate crimes would not be tolerated on Sydney's streets and the necessary police resources would be put in place to catch those responsible.
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