Parents also protested outside Sambodi Primary School northeast of Colombo against the boy's admission after he turned up for his first day of class, the official said.
"Parents don't want their children to be in the same school with this six-year-old boy," regional education director Saman Wijesekera told AFP.
Sri Lanka has a national HIV/AIDS awareness programme but understanding of the disease and how it spreads is low, leading to frequent cases of stigma and discrimination against sufferers.
The boycott by all of the school's 179 students is the latest blow for the child and his mother, who has been trying since last year to find him a school to attend.
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She said a string of schools had refused her only son a place after false rumours spread in her village last year that her husband had died from AIDS. He died of tuberculosis and kidney failure.
Sambodi's headmaster agreed last week to admit the boy after intervention by authorities, the mother told AFP by phone.
"Only after I complained to the child protection agency did they intervene and got him into this school," she said.
She said lawyers had filed a case in the Supreme Court for compensation for trauma caused to her and her son.
The mother, who is a casual labourer, said she has been unable to find work in the village after the false rumours and media coverage of the ostracism of her child.
Wijesekera said parents of Sambodi along with health and legal experts were set to hold a meeting on Wednesday to discuss the boy's admission.
Sri Lanka has few cases of HIV -- 2,073 at the end of 2014 with 29 of them below the age of 14, official figures show.
Pupils at a school in Sri Lanka have all boycotted classes after rumours circulated that a 6 year old was infected with HIV AIDS
— IKOTE (@IkoteBrian) February 29, 2016
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