In The Legend of Zelda: Ocarina of Time 3D for the Nintendo 3DS, you can unlock the new Boss Challenges to replay any boss you’ve already beaten.
To unlock Boss Challenges, you first just need to beat the bosses as you would normally in the story. Once you’re an adult, before you learn the Prelude of Light, talk to Sheik and she will tell you that you can rest in your house to relive past battles. She’s referring to the Boss Challenges.
Return to your house and rest in the bed. You’ll be able to fight any bosses you’ve already played. Once you beat all of the bosses in the Boss Challenge, you’ll unlock the last challenge, which is to fight all bosses in order.