Jaydan Patterson, 13 and Tyler Rolani, 11, who both have learning difficulties left their school at Warwick Farm, south west Sydney, at 10.35am Monday morning.
The pair were caught on CCTV boarding a train at Warwick Farm station before being spotted at around noon at Town Hall station.
The pair appear to have become separated after Tyler was seen aboard a train towards Flemington, while Jaydan was seen in the Airds area.
Police say Jaydan has dark hair and freckles and is believed to be wearing three-quarter length short, a dark polo shirt. Tyler is wearing pink shorts and a baby blue polo shirt. Both boys were wearing backpacks.
Police are asking anyone with information as to the whereabouts of the boys to call 000 immediately.
Image via Sydney Police