Japanese film with kids who grew up together learning how to become assisins, one and only girl and one boy survived after many battles. The last battle the girl cuts off the man head who wants her dead.

Maybe Shinobi: Heart Under Blade? My other guess would be Ninja Assassin.

I think your on about

AZUMI

Have look at the YouTube trailer clip

http://www.youtube.com/watch?v=AWOJw7sPatA