Students cried as they arranged the tributes at the foot of a sycamore tree outside the entrance to Heathside School in Weybridge, Surrey.
Educational psychologists attended to help pupils come to terms with the loss of the popular 13-year-old, known as Milly.
Meanwhile, police with sniffer dogs continue to search the woodland in Hampshire where the teenager's body was discovered.
Surrey County Council local educational officer John Ambrose said the end to the uncertainty over Milly's fate may have helped the school's 1,300 pupils because they now knew what had happened.
"But that doesn't stop people from feeling very sad and sorrowful," he said.
"There are the whole range of human emotions here that you would expect - sadness, anger, annoyance, concern.
"We do still need to find a way to move the school forward."
'Amazing friend'
Nearly 150 bouquets had been left at the school on Monday morning and over the weekend.
A group of students huddled round the tree with heads bowed shortly before starting their lessons.
Messages on the cards included one from a close friend named Sophie, who wrote: "I miss you so much.
"You were an amazing friend and you will always hold a place in my heart."
But a more sombre note read: "Beautiful Milly, Such an abrupt end.
"We will live in fear until the monster is caught. RIP."
Another card read simply: "WHY?"
Public help
Search teams are continuing investigations at Yateley Heath forest in Minley, near Fleet in Hampshire, where Milly's remains were found.
A Surrey Police spokeswoman said six dogs, trained in the recovery of human remains, returned to the isolated spot on Monday morning.
Milly's body was discovered on Wednesday, six months after she vanished from Walton-on-Thames railway station on her way home from school.
Police have received hundreds of calls from the public since her remains were found.