The 29-year-old faced court on Saturday and was refused bail to reappear next month.
He has been accused of one count of rape and one count of indecent treatment towards a child under the age of 16.
The man also faces two charges of possessing child exploitation material and another of creating such material featuring the involvement of a child.
The childcare centre where he worked prior to his dismissal in Brisbane's north emailed parents and carers on Saturday morning.
"We appreciate that this news will be distressing for families," said the message, a copy of which has been seen by AAP.
"We want to be open and honest with you and keep you informed."
It confirmed the man's arrest came after a formal complaint earlier in the week which led to a police investigation.
"The employee was stood down on the day of the complaint and their employment was terminated on Thursday," the email said.
It said the centre had already contacted a small number of families involved with the centre and confirmed the man had worked with older children.
"We are all shocked and distressed by this news," it read.
The matter follows unrelated allegations that a 45-year-old Queensland man abused 91 children while working at 10 childcare centres in Brisbane, one in Sydney and another centre overseas between 2007 and 2022.
He is currently before the courts and facing more than 1600 charges.
Queensland Attorney-General Yvette D'Ath told a parliamentary estimates hearing earlier this month the state's blue card screening of the alleged prolific Gold Coast offender did not return any red flags.
"Before anyone is issued with a blue card, a national criminal history check is undertaken for every blue card application in Queensland," she said.
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