She chose a book featuring Prince George's "favourite character" Fireman Sam, and a Beatrix Potter Tom Kitten figurine for Princess Charlotte.
The gifts cost Â£10 in total and Sarah Throssell, who served her, said she seemed "really pleased with the finds."
The Duchess was opening East Anglia's Children's Hospices shop in Holt, Norfolk, as patron of the charity.
Updates on this story and others from Norfolk
Rebekah Hughes, who has Dravet Syndrome, a severe form of epilepsy, took the duchess on a tour of the shop.
The Duchess also helped volunteers sort clothes in a back room and revealed her frustration with security tags, saying: "they're a nightmare to get off."
She told staff she often buys cook books in charity shops.
The new shop is about 20 miles from the home Catherine shares with her husband and children at Anmer Hall.
It was her latest engagement on behalf of the charity after she launched a drive to raise Â£10 million for a new hospice in Norfolk in 2014.
She delivered her first public speech as the Duchess of Cambridge in 2012 when she opened its Treehouse hospice in Ipswich.
The charity, which has three hospices in Cambridge, Norfolk and Ipswich, offers support to more than 700 children, young people and family members.
The Duchess of Cambridge bought presents for her two children as she opened a new charity shop.