The stabbing at Christ the Good Shepherd Church in Wakeley left Bishop Mar Mari Emmanuel and a priest hospitalised after the 16-year-old's alleged attack during a live-streamed sermon on Monday night.
Investigators from the Joint Counter Terrorism Team Sydney interviewed the boy in hospital on Thursday and charged him with committing a terrorist act.
The offence carried a maximum penalty of imprisonment for life, police said.
The boy was refused bail and is expected to appear before a bedside court hearing on Friday.
Bishop Mar Mari Emmanuel was allegedly stabbed during a church sermon. (HANDOUT/Christ of Good Shepherd Church)
The Joint Counter Terrorism Team Sydney includes members of NSW Police, Australian Federal Police, ASIO and the NSW Crime Commission.
The charge comes as investigators hunt for as many as 50 people involved in a violent riot that unfolded after the incident.
Dozens of police were injured, their cars vandalised and a cohort of officers and paramedics were forced to shelter inside the place of worship.
NSW Police Commissioner Karen Webb said many people who turned up for the commotion were not members of the church community.
"(What) has been shown is that people just came along to participate in a riot and that's disgraceful and disgusting," she said.
The commissioner said 50 people were wanted for questioning over the unrest, including several who disguised themselves, and police were looking for public help to identify them.
"People in the community know who they are, their families know who they are, and we need to know who they are," she said.
Dani Mansour, from Doonside, is the first person to be charged over the public disorder incident.
Appearing in court on Thursday, the 19-year-old said he made a mistake but he was "pissed off" at officers who had hurt people outside the church.
Mansour allegedly filmed himself kicking two police cars during the riot before uploading the footage to Instagram.
Speaking to reporters outside Blacktown police station on Thursday, he said he had "just done one (police car)".
He will next face Blacktown Local Court on May 2.
The bishop has said he forgave his accused assailant and called on his followers to obey the law following the riot.
"I need you to act Christ-like, the lord Jesus never taught us to fight," he said in an audio message released by the church on Thursday.
The attack was declared a terrorist act because of the teen's possible religious motivation.
NSW Premier Chris Minns met religious leaders on Thursday to call for calm and cohesion.
"We've come together because we need to, and the message that's been sent from community leaders is one of compassion, understanding, cohesion, unity and most important peace," he said.
The premier stressed the importance of faith leaders in imparting instruction and wisdom to the millions of people across NSW who will attend their local churches and mosques to be amongst their community.
"They'll go there for solace and for strength," he said.
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