The two pupils were believed to be in the same year group at Ashford Church of England Primary School.
The pair caught the rare invasive group A streptococcal infection (iGAS), the UK Health Security Agency (UKHSA) said. The government agency said it had recommended staff and pupils be prescribed antibiotics.
The child who died is believed to be six years old and in Year 1.
Dr Claire Winslade, health protection consultant at UKHSA South East, said: “We are extremely saddened to hear about the death of a pupil at Ashford Church of England School, and our thoughts are with their family, friends and the school community.
“As a precautionary measure, we have recommended antibiotics to pupils and staff in the same year groups as the individuals affected. We have provided advice to the school to help prevent further cases and will continue to monitor the situation.
“Information has been shared with parents about the signs and symptoms of iGAS, which include high fever with severe muscle aches, pain in one area of the body and unexplained vomiting or diarrhoea. Anyone with these symptoms should call NHS11 immediately.”
Infection with group A Streptococcus bacterium usually causes a sore throat or skin rash and is passed by physical contact or through droplets from sneezing or coughing.
In very rare cases, the infection can become invasive and enter parts of the body where bacteria aren’t normally found and can cause severe and life threatening diseases such as necrotizing fasciitis and streptococcal toxic shock syndrome.
A spokesman for the UKHSA said: “Specialists are arranging for antibiotics to be offered to pupils and staff at a Surrey school as a precautionary measure, following two cases of invasive Group A streptococcal infection (iGAS).
“Sadly, one pupil from Ashford Church of England Primary School has died and another is in hospital, but showing positive signs of recovery.”