Marguerite was born in Angoulême on 11 April 1492, the eldest child of Louise of Savoy and Charles, Count of Angoulême. Her father was a descendant of Charles V, and was thus the successor to the French crown by masculine primogeniture, if both Charles VIII and the presumptive heir, Louis, Duke of Orléans, were unable to produce male offspring.
On 16 February 1488, her father, Charles, married eleven-year-old Louise, the daughter of Philip II of Savoy and Margaret of Bourbon, who was the sister of the Duke of Beaujeu. Louise was considered one of the most brilliant feminine minds in France and she named their first-born, "Marguerite", after her own mother.
Two years after Marguerite's birth, the family moved from Angoulême to Cognac, "where the Italian influence reigned supreme, and where Boccaccio was looked upon as a little less than a god". Marguerite's brother, Francis, later to be King Francis I of France, was born there on 12 September 1494.
She had several half-siblings, from illegitimate relationships of her father, who were raised alongside Marguerite and her brother. Two girls, Jeanne of Angoulême and Madeleine, were born of her father's long relationship with his châtelaine, Antoinette de Polignac, Dame de Combronde, who later became Louise's lady-in-waiting and confidante. Another half-sister, Souveraine, was born to Jeanne le Conte, also one of her father's mistresses.
Her father died when she was nearly four; her one-year-old brother became heir presumptive to the throne of France. Thanks to her mother, who was only nineteen when widowed, Marguerite was carefully tutored from her earliest childhood and given a classical education that included Latin. The young princess was to be called "Maecenas to the learned ones of her brother's kingdom". "Never", she wrote, "shall a man attain to the perfect love of God who has not loved to perfection some creature in this world." When Marguerite was ten, Louise tried to marry her to the Prince of Wales, who would later become Henry VIII of England, but the alliance was courteously rebuffed. Perhaps the one real love in her life was Gaston de Foix, Duc de Nemours, nephew of King Louis XII. Gaston went to Italy, however, and died a hero at Ravenna, when the French defeated Spanish and Papal forces.