Charles Tudawali was visiting people at Munja Station, about 350km northeast of Derby, in December 1976 when he went out with a group of older boys to catch horses.
But Charlie wandered off on his own after a disagreement about how to find their way back to camp, the WA Coroner's Court heard on Tuesday.
Indigenous trackers from the area helped with an extensive air and land search for the 13-year-old over several days and believed it was likely Charlie had been taken by a crocodile.
"At the time that Charlie disappeared, this particular area had several waterways which were likely infested with crocodiles, and the area was known to have wild dingoes and snakes," counsel assisting the coroner Lyle Housiaux said.
The court heard the boy had a mental disability, epilepsy and no bushcraft skills, and his family believe he was dead.
Coroner Sarah Linton will hand down her findings at a later date.