While it was planned that both Prince William and Kate Middleton would drop the 4-year-old at school, only the father was present.
The school has 560 pupils between the ages of four and 13.
Prince George on his first day at the Westacre Montessori nursery school near Sandringham in Norfolk.
Prince George started school today, but his mother - The Duchess Of Cambridge, was too unwell to take him.
It was announced in March that Prince George will attend Thomas's school in Battersea, a choice that came as a surprise as many speculated that the little prince will attend the same school where his father and uncle studied.
Along with his classmates, he will spend the day getting to know teachers, adults and other children as well as completing the important task of finding his classroom peg.
On Monday, the palace revealed the Duke and Duchess were expecting their third child, and confirmed Kate had suspended all royal duties due to her illness.
Prince George politely shakes her hand and then quickly grabs his dad's hand again.
George turned four on July 22 and will therefore be one of the youngest in his year as British children start their schooling in September after their fourth birthday.
George will be dressed in a smart new uniform, comprising a navy v-neck pullover, matching Bermuda-style shorts, long red socks and black shoes.
A day later William said Kate was well, adding: "There's not much sleep going on at the moment".
The $23,000 a year school teaches a range of traditional subjects along with ballet, art, drama, French, music and physical education. It's always a bit anxious to start with, but she's well'. George, who will start in one of three reception classes, will also be able to play in the "imaginative rooftop playground" while outdoor activities are also held at nearby Battersea Park, Barns Elms and the Wandle Centre. William and Harry attended Ludgrove School in Berkshire before heading to boarding school at Eton College near Queen Elizabeth's home at Windsor Castle.