The boy, described as having a dark complexion, of slim build, about 30kg with dark hair and closer in size to a six- or seven-year-old, was last seen at 3.15pm on the corner of Luxmoore Rd and Selwyn St.
He was found at the bridge 45 minutes later.
Police would not disclose the extent of his injuries, but said the boy "had certainly suffered some trauma", including injuries to his face and is understood to have significant amount of blood on his school uniform.
He remained at Timaru Hospital, in a comfortable condition, but he hadn't spoken to family or police about what happened.
On Thursday he was wearing dark blue polarfleece, dark blue shorts, a teal polo shirt and multicoloured backpack.
Police are appealing anyone with information to contact Timaru police.