The Ninja Academy will always be in your home country .
Example: If you're a Sound Ninja, it will appear in Otogakure.
The Ninja Academy is a place you'll visit quite a lot. It is the place where you will fight your master to level up, the main point of the game.
To fight your master, you must gain enough experience to fill your experience bar (it will turn blue once full). Your master will be the same level as you and will have similar attack and defense (note that you cannot use an buffs against your master).
Once you beat your master, you will level up and gain 1 attack, 1 defense, and 10 hitpoints.
In the Ninja Academy you may change your specialty for a small amount of gold (exact amount based on your level) and you may also unsummon or summon your mount which is useful if you'd like to save your mount's rounds for Kabuto or Orochimaru.