In August, Harry and his family relocated to Britain after six years of living in California, with seven-year-old Prince Archie, and five-year-old Princess Lilibet, starting school in September.
The location of their new home and details of the children's school have been kept private.
On Monday, a spokesperson for the Duke and Duchess of Sussex, confirmed reports that Archie and Lilibet were changing schools after just two days.
The distance between their home and the original school, with heavy traffic in the area, had caused concern.
"The decision for the children to move school was taken following a discussion with the family's security team about the practicalities of their current arrangements," the spokesperson said.
"The parents remain extremely grateful to all the teachers and staff for the love, care and effort they have shown their family. This decision should in no way be interpreted as a reflection on the school or the exceptional care the children have received there."
The couple stepped down from royal duties and moved to the US in 2020, leading to estrangement and awkward relations with the royal family as they delivered a series of barbed comments about the institution.
Their return came as a surprise, with even the monarch unaware of their plans until just days before it became public.
The announcement came just a day after Meghan posted on Instagram the first glimpse of the family's new life in Britain, sharing footage of Harry and the children enjoying an apparently idyllic spell in the English countryside..
Harry and Meghan are not living in a royal residence and will remain non-working royals, as agreed with the late Queen Elizabeth before their move.
Their status as private citizens was confirmed in a letter authorised by King Charles and sent to senior British officials last week, a step which their spokesperson said had come as a surprise to Harry and Meghan.
The prince has also been critical of the government's decision to strip him and his family of automatic police protection afforded to other senior royals, with a bespoke system put in place instead.
Harry's security is currently being reviewed by a government committee, and the couple's spokesperson confirmed that Meghan's situation is also being looked at again for the first time since they moved away from Britain.
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