An Imperial Household Agency official told reporters Kiko had given birth by a Caesarean operation to the 2,558 gram (5 lb 10 ounce) boy at 8:27 a.m. (2327 GMT).
He said both Kiko, 39, and the baby were doing well.
No imperial boys had been born since the baby's father, Prince Akishino, in 1965, raising the possibility of a succession crisis. Crown Prince Naruhito, 46, and Crown Princess Masako, 42 have one child, 4-year-old Princess Aiko.
SAKE TOASTS, CEREMONIAL SWORD
Ceremonies around the birth include the laying of a tiny sword near the baby's pillow by his father to ward off demons.
Japanese emperors have not been worshipped as gods since Akihito's father, Hirohito renounced his divinity after Japan's defeat in World War Two, and have no political authority.
But the monarchy remains rich with symbolism and ritual.
Near Tokyo's Gakushuin University, where Akishino and Kiko met, a dance troupe performed, carp streamers flew in honor of the infant boy, and locals toasted the baby with sake rice wine.
"It's good that a boy was born so that the royal family could keep its male lineage. I'm happy that Japan's tradition has been maintained," said Tadayuki Aman, a 77-year-old doctor.