Where to Start?

Recommended Starting Stats: Novice
It is strongly advised that you DO NOT start a ninja as Ninjutsu Build. They have horrible MATK at the beginning and you'll only do 3 - 15 damage per spell.
Get to job 10 Novice in the Novice Training Grounds.
Str: 9 (15+ when you leave the novice arena)
Agi: 9 (12-15 when you leave the novice arena)
Vit: 1 (no change)
Dex: 9 (11-12 when you leave the novice arena)
Int: 1 (no change)
Luk: 1 (never ever change)

First Stats: Ninja lvl 12-14
Best choice to start off, is a Pure throwing build. It costs small SP. Shurikens are fairly cheap. You only really need 1 stat. Throwing build is based on Str & your Weapon's ATK. Shuriken & Kunai CANNOT miss, no matter what your dex is.
Level to 25 - 30 in Payon Dungeon Level 1.
Str: 40+ (Pure Str, little Dex & agi)
Agi: 20 (Higher aspd slightly decreases Delay between shurikens)
Vit: 1 (no change)
Dex: 15 (15 only needed to hit the bare minimum enemies in payon until you get Throw Shuriken)
Int: 1 (no change)
Luk: 1 (never ever change)

Mid Stats: Ninja lvl 30 - 55
Get pure Str and skills that increase damage of Throw Shuriken (Toubidogou Shuuren/ "Throwing Dagger Practice" for the mentally challenged. How many daggers does a ninja throw, huh?). Make sure that you get/have Utsusemi (CSS) Lv5 to avoid any physical damage.
Level to 55 - 60 in Toy Factory Level 2.
Str: 65+
Agi: 25-35
Vit: 1
Dex: 20
Int: 1-10
Luk: 1

Adv Stats: Ninja 65+
At this point you can reset to Ninjutsu build or Continue with Shuriken & Kunai Build.
Throwing Build: 65 - 97 in High Orcs (Ice Kunai/Murasame[2] with Shuriken).
Ninjutsu Build: 65 - 97 in Kiel's Factory 01. No monsters use magic. They give rare and useful equipment. High Exp.
Throwing Build:
Str: 99
Agi: 55-60
Vit: 1
Dex: 20
Int: 15-25
Luk: 1

Ninjutsu Build:
Str: 1
Agi: 1
Vit: 1
Dex: 90-99
Int: 85-95
Luk: 1

Final Stats: All Builds 96-99
96 to 99 for all builds can be made on quests alone. See: http://irowiki.org/wiki/Quests" http://irowiki.org/wiki/Quests
Otherwise, Continue Levelling in Kiel01. With 99 Int, a Ninjutsu Ninja's weakness to magic is greatly reduced.
Throwing Build:
Str: 99
Agi: 70+
Vit: 1
Dex: 30
Int: 25-35
Luk: 1

Ninjutsu Build:
Str: 1
Agi: 1
Vit: 15
Dex: 99
Int: 99
Luk: 1

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Ninja's Equipment:
Pretty Straight-foward. If you're going Throwing Build: Get Str & Agi boosting equipment. If you're going Ninjutsu Build: Get Int & Dex boosting equipment.

Levels 1-12: Novice Arena
Basic Supplied Novice Gear.

Levels 12 - 25: Payon Dungeon
Headgear: Pirate Bandana, Munak Hat, Kitsune Mask, Angel Wings, Evil Wings, Ghost Bandana, Sakkat, Vanberk carded Headgear (str +2).
Shield: Arm Guard/Gauntlet (bought from Ninja Guild 10k)
Weapon: Stilleto[2]/[3] (Wolf carded, if you have any spare)
Armor: Panties (Zerom Drop)
Garment: Undershirt (Pasana Drop)
Footgear: Pretty much any footgear will do. (Matyr Carded Shoes[1] If you have some)
Accessories: Brooch or Ring

Level 26 - 55: Toy Factory
Headgear: Previously mentioned.
Armor: Panties or Ninja Suit
Garment: Undershirt, Ancient Cape, Nine Tail/Bapho Jr carded Muffler, Morpheus' Shawl.
Weapon: Triple Wolverine Stilleto[3], Double Wolverine Damascus[2]. (Zipper Bear works too, but costs more SP)
Shield: Arm Guard[1], Improved Arm Guard[0]/[1]. (Card it with whatever you want)
Footgear: Shoes[1] (Card it with whatever you want)
Accessory: Shinobi Sash, Ring &/or Brooch. (2 Shinobi Sashes does not double the combo effect)

Level 60 - 96: Throwing Build - High Orcs/Kiel Dungeon.
Headgear: Previously Mentioned + Evil/Angel Wing Ears.
Armor: Panties/[1], Ninja suit/[1], Odin's Blessing[1].
Garment: Undershirt/[1], Nine Tail/Bapho Jr carded +9 Muffler[1], Morpheus' Shawl, Falcon Muffler, Vali's Manteau.
Weapon: Triple Wolverine Stilleto[3], Double Wolverine Damascus[2]. (Zipper Bear works too, but costs more SP)
Shield: Arm Guard[1], Improved Arm Guard[0]/[1], Valkyrie's Shield[1] (Card it with whatever you want - Yes, Ninja can use valk shield. It's not a Trans-only item, like the rest of the set)
Footgear: Freya's Shoes or Vidar's Boots.
Accessory: Shinobi Sash, Ring/Ring of Muscle[1] (Mantis), Brooch/Coward's Brooch[1] (Shinobi).
~--~
Level 60 - 96: Ninjutsu Build - Kiel Dungeon.
Headgear: Apple of Archer, Frigg's Circlet, Morpheus's Hood, Magni's Cap, Isilla Carded Headgear.
Armor: Ninja suit/[1], Odin's Blessing[1].
Garment: Morpheus' Shawl, Vali's Manteau.
Weapon: Triple Dexterous Ashura[3]. (Drops card)
Shield: Improved Arm Guard[1], Valkyrie's Shield[1], Stone Buckler[1]. (Valk & Stone buckler makes useful combos. Valk/odin/frigg more-so than magni/stone/odin.)
Footgear: Freya's Shoes or Vidar's Boots.
Accessory: Shinobi Sash, Earring[0], Celebrant's Mitten, Glove or Coward's/Nimble Glove[1] (Shinobi/Zerom), Morpheus' Ring, Morpheus' Bracelet.

Note: Never wear the whole Morpheus Set, it's advised to leave one of the accessories off. The full set gives uninterruptable cast but cast time +25%. With Utsusemi active you won't get hit, so it won't be interrupted anyway, you'll just get more cast time.
Make sure to wear your equipment in combos, It's pointless to have stone buckler/vidar without the rest of the combo.

96-99 is basically the same.

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Ninja Skills:
Time to show off your fancy Kung Fu.

Throwing Ninja:
Tobidogou Shuuren: Level 10
Throw Shuriken: Level 10
Throw Kunai: Level 5
Tatamigaeshi: Level 1
Kagetobi: Level 5
Utsusemi: Level 5 (All Ninja Must have this skill)
Mist Slash: Level 1
Ninpou Shuuren: Level 10
Nen: Level 10
Do what you want with the rest. Throw Fuuma Shuriken Sucks, Don't get it.

Ninjutsu Ninja:
Ninpou Shuuren: Level 10
Hyousensou: Level 10
Kouenka: Level 7 - 10
Tatamigaeshi: Level 1
Kagetobi: Level 5
Utsusemi: Level 5 (All Ninja Must have this skill)
Kaenjin: Level 7
Nen: Level 5
Bakuenryuu: Level 5
Do what you want with the rest.
Notes: Hyousensou ("Lightning spear of ice" for stupid people) is a Ninja's best spell. Except for the fact that Siroma and other spell enhancing cards don't affect it. Base-wise it's stronger than Cold bolt by 10%. Fuujin is 1/2 the strength of Lightning Bolt, Kouenka is 3/4 the strength of Fire Bolt. Fair, huh?
Kaenjin can slow any monster by 95%, while inflicting damage.
Suiton increases Hyousensou's damage by 15%, and slows the enemy by 40%.
Raigekisai is bugged and is completely worthless.
Grade 3 Ninjutsu Spells: Hyoushouraku & Kamaitachi are completely useless. Do not get them.
Bunshin no Jutsu does not stack with utsusemi, has higher cost, cast time and it screws your color palette up.

Against a Non-magic using MVP, a Ninja can do quite well.
Against any kind of PvP-built other class character, a Ninja will most likely get his ass handed to him. Unless he/she's specifically built to take down that particular class.