The 16-year-old was arrested in Western Australia after allegedly posting he would "Christchurch 2.0" the Australian Islamic House at Edmondson Park in southwestern Sydney.
The comment on the Instagram account of the place of worship appeared to refer to the massacre of 51 worshippers at a New Zealand mosque in 2019.
The sixth anniversary of the murders, carried out by an Australian man, will fall in a few weeks.
The teen was charged on Wednesday with creating false apprehension to the existence of threats or danger, NSW Police said.He was granted conditional bail and is due to appear in a WA children's court in April.
The post was made during the first week of the Muslim holy month of Ramadan.
Community leaders say the latest incident is far from an isolated example of Muslims being targeted with hate.
"The threat is deeply concerning towards the Muslim community," Grand Mufti Riad El-Rifai told AAP on the steps of the mosque.
"But the message coming from mosques across all of Australia is one of mercy, love and brotherhood.
"Australia is a safe and secure country and we don't want people to further inflame this situation and tear its social fabric."
Sheik El-Rifa, a respected Islamic scholar who migrated to Australia from Lebanon two decades ago, said violent sectarian rhetoric had increased towards Muslims since Israel's offensive in Gaza.
But Australia's strength lay in its multicultural principles and the ability of good people to "help move society beyond demonisation and violence", he added.
Lebanese Muslim Association secretary Gamel Kheir said the tight-knit Islamic community had rallied together after the threat against the mosque.
"Sadly it's not the first event nor an isolated event," he told ABC radio.
In a pointed message to political leaders, Mr Kheir warned the use of inflammatory language could embolden the public.
"Politicians need to stop playing political football with the idea of anti-Semitism and Islamophobia," he said.
"For politicians to come out blatantly ... only enables and emboldens these comments made allegedly by a 16-year-old child."
There has been a marked spike in reported incidents of Islamophobia and anti-Semitism, amid simmering tensions over the turmoil in Gaza.
However, community leaders have praised the swift police response and allowing prayers to continue with the assurance of their presence.
Police said they did not believe there was an ongoing threat to the community.
Australian Islamic House president Mazhar Hadid said places of worship needed to be safeguarded from hatred and violence.
"We are profoundly concerned by this threat and take it with the utmost seriousness," he said.
"We also urge the public to remain vigilant and to stand united against Islamophobia and all forms of bigotry."
Deputy Prime Minister Richard Marles joined other politicians and religious figures in condemning the "appalling reference" to the Christchurch attack.
"There is no place for Islamophobia in our nation and it's really important that we are standing with that community today and we are calling this out for what it is," he told ABC TV.
Prime Minister Anthony Albanese and NSW Premier Chris Minns have vowed whoever was responsible for the threat would face the full force of the law.
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