The 14-year-old opened fire on Friday morning at Debsirin Nonthaburi School in Nonthaburi province northwest of the Thai capital before apparently taking his own life.
He also appeared to have killed his two grandparents at his family home earlier in the morning, officials said.
The girl, 12, died after hospitalisation, the health ministry said.
The school had posted a message on Facebook on Friday seeking blood donations for two students, including the girl, who was in seventh grade.
Fourteen people remain hospitalised, of whom seven remain in critical condition on Saturday.
Most of those wounded were between 12 and 14 years old.
Relatives claimed the bodies of eight people from Bangkok's Institute of Forensic Medicine: five school staff, the accused shooter, and his grandparents.
Emergency workers brought out a coffin and loaded it onto an ambulance, which will transport the bodies to their home towns for funeral rites.
The young girl's body is still to be released.
Wiroon Supasingsiripreecha, head of the institute, said most of the victims suffered a single fatal gunshot wound to a vital area, including the chest or head.
He said the gunshot wound found on the alleged shooter was consistent with the weapon he had used.
Officials said the gun, described as small and compact, was legally registered to the boy's grandfather.
There were reports that the boy, who lived with his grandparents, had shown signs of stress connected to school, although some of his relatives told Thai media that they were unaware of any troubles he might have been facing.
The co-educational state school, which has about 3,000 students enrolled aged 12 to 18, said all classes would be suspended between August 10-14 and school staff were instructed to work from home during that time.
A few mourners laid flowers Saturday morning at the school's gate, where a few police officers could be seen.
Charin Siriananchai brought his two sons, ages nine and six, to pay their respects.
He said while his sons do not study here, he lives in the neighbourhood and drives past this school almost every day, often stopping to allow students to cross the road.
"Everyone was saddened and shocked, because it was unexpected that this would happen in Thailand, and also it's quite a great loss," he said.
Some parents also came with their children to collect their belongings left behind after the shooting.
A father, who declined to identify himself, said his son, who was at the school during the shooting, was still in shock and could not sleep alone.
Thailand has one of the highest rates of gun ownership in Asia, second only to Pakistan and far surpassing its Southeast Asian neighbours.
Thailand had 3.49 deaths by firearms per 100,000 people, according to 2023 statistics published by World Population Review.
That puts it well behind parts of Latin America and the Caribbean, but relatively high in Asia.
Only the Philippines is higher in Southeast Asia.
While shootings involving indiscriminate killings are not common, the country has seen an uptick in high-profile shooting deaths in recent years.
In February, a 17-year-old stole a gun from police and opened fire at a public high school in southern Thailand, briefly taking people hostage in a two-hour attack that killed one person and wounded two others.
A 14-year-old boy was accused of a 2023 shooting at a major Bangkok shopping centre.
