The 13-year-old has not been found for three days despite an "intensive search" police said.
The Year 8 Ark Globe Academy pupil was thought to have been travelling with a friend on a bus at 8am on Tuesday morning (April 23) but did not arrive at his school in south London.
In a letter to parents on Wednesday, executive principal Matt Jones said the boy was in full school uniform but exited near the bridge, before his usual stop closest to the school in Elephant and Castle.
Mr Jones said in his letter: “It is with worry that I share news about (the pupil’s name), a Year 8 student at Ark Globe Academy.