Leon Williamson, 12, and Olivia Bryson, 14, were last seen at Glengarnock railway station in North Ayrshire, boarding a train to Glasgow at about 9.15am on Tuesday.
Police Scotland have now confirmed that Leon has been traced, although the search for Olivia continues.
Sergeant Allen Dodds said: “We are pleased to confirm that Leon has been traced safe and well. However, we remain focused on trying to find Olivia.
“We are checking a possible sighting of her in the Manchester area; however, if anyone has seen Olivia or has any information of knowledge as to her whereabouts, please contact police.
“We need to know she is safe and well.”
Both children live in residential accommodation in the Ayrshire area.
Olivia has family in Manchester and it is thought she may have gone to visit them.
Police Scotland officers are liaising closely with other officers from British Transport Police and Greater Manchester Police.
Olivia is about 5ft 2in and of medium build, with blue eyes, freckles and brown hair which she usually wears in a ponytail.
She was wearing dark jogging trousers and a North Face jacket, which is grey at the top and dark-coloured at the bottom.
She tends to wear a black baseball cap on her head with her jacket hood up and has an English accent.
Officers urged anyone with information to call Irvine police station via 101, quoting incident number 0795 of May 22 2018.