Specialist officers from the City of London Police, who are treating it as a missing persons case, have been leading the probe for the year 8 student after he fell into the river just after 8am on Tuesday.
The Ark Globe Academy pupil was said to have been travelling with a friend on a bus in the morning but did not arrive at the south London school.
Instead witnesses have told the Sun they saw the boy fall into the River Thames before one brave onlooker waded into the water to try to save him.
But the woman was only able to retrieve his schoolbag, the Sun reported.
In a letter to parents on Wednesday, executive principal Matt Jones said the student was in full school uniform but exited near the bridge, before his usual stop closest to the school in Elephant and Castle.
He then “fell” into the River Thames, Mr Jones added.
City of London Police confirmed it was leading an investigation into a missing person, linked to an incident where a child fell into the river from Tower Bridge.
The force said despite an “intensive search” by officers, helicopter and marine units, the boy had not yet been found.
A City of London Police spokesperson confirmed the force was working with the Metropolitan Police as part of the “missing person” investigation.
The spokesperson said: “We believe this is linked to an incident where a child fell into the Thames from Tower Bridge.
“Despite an intensive search by City of London Police, the police helicopter and marine units, this person has not yet been found.”
Anyone who witnessed the incident on Tuesday April 20 at 8.09am, should call the police on 020 7601 2999, quoting reference 21000215310.