"Hisa" means serenity while the Chinese character "Hito", traditionally used for heirs to the throne, means "the highest moral standard."
As part of the ceremony, Prince Akishino, the boy's father, wrote the boy's name on handmade paper that was then placed inside a wooden box and laid by the child's pillow in a brief ceremony known as Meimei no Gi.
Princess Kiko also placed in the box a paper marked with an umbrella pine tree - a unique royal crest that Hisahito will use for life.
The boy, born on September 6, is third in line to the Chrysanthemum throne, after Crown Prince Naruhito and his father Akishino.
He is the first boy born to the royal family since his father - who is also known as Fumihito - in 1965.
Kiko's surprise pregnancy delighted conservatives as it came when the government looked set to allow a female monarch to end a looming succession crisis.