In order to become a Ninja, you must be a novice at job level 10. A short quest is required before you will be able to change jobs.
1. The Ninja guild is located in the city of Amatsu.To get to Amatsu, an NPC near the wall north of the merchant guild at 8 o' clock direction in Alberta will take you there for free (location is 30, 64).
2. Enter the Ninja guild building located in the center of Amatsu (147, 136).http://i5.photobucket.com/albums/y189/renz012/screenSakray045.jpg
3. Inside the building, you won't see anyone. You'll have to move past the hidden wall at the back of the main room. http://i5.photobucket.com/albums/y189/renz012/screenSakray048.jpg
4. Inside the real guild room, talk to the guild master Couger Kai, and tell him you wish to join. He's a little wierd, but he'll ask you to deliver notice to his enemy who is hiding out in the highest point in Einbroch.
5. Make your way to the Einbroch Tower. The cheapest way to get to Einbroch would be to go back to alberta via boat (free), take the boat to izlude (500z)
Board the airship to Juno (1200z)
In Juno switch from international to domestic flight (if you do it right, free)
And then get off at einbroch.
In einbroch, near the center tower there will be several NPC's that will allow you to go to the top of the tower for 10 zeny.http://i5.photobucket.com/albums/y189/renz012/screenSakray073.jpg
6. At the top of the Einbroch Tower, you'll find a young man. Talk to him, and he will ask that you bring 5 Cyfar and 1 Pracon.http://i5.photobucket.com/albums/y189/renz012/screenSakray088.jpg
7. When you give him the items, he will reveal himself as the person you were supposed to give the letter to. He'll give you a reply, and warp you to Amatsu. At this point return to Couger Kai in the ninja guild.
8. Kai will ask you bring him him 5 Cyfar and 1 Pracon now. You simply need to have these items on you, he will not take them from you.http://i5.photobucket.com/albums/y189/renz012/screenSakray108.jpg
9. Once you have the items he asked for, you'll be class changed to Ninja.http://i5.photobucket.com/albums/y189/renz012/screenSakray120.jpg
Note:The Guide came from Doddler and thanks to Lix Tetrax of Ragnaboards for the screenshots