His lawyer declined to comment outside the court.
Police will allege the man enticed a 4-year-old girl and 5-year-old boy from a holiday school care program in North Perth on April 19, sparking a two-day manhunt.
He was charged on April 21 with three counts of sexual penetration of a child under 13 and two of deprivation of liberty.
Police searched a North Perth home in relation to the investigation.
CCTV released from a property on Angove Street the day after the incident showed a man walking with the boy and girl following behind him not long after he managed to allegedly lure them out of a nearby childcare centre.
The children were found alone in the playground in Hyde Park about 12.15pm, about an hour after they went missing from a holiday care program, whose staff had not noticed they were gone.