Police allege the man indecently assaulted a girl who was aged 10 to 12 when he was a priest at St Aloysius Church in Shenton Park in 1980.
They claim the same priest was working at the Holy Name Church in Carlisle in 1969 when he indecently assaulted a girl aged six to seven.
The offences allegedly occurred at the presbytery.
The man has been charged with six counts of indecent dealing with a child under 13.
He is due to appear in the Perth Magistrates Court on Tuesday.