There is no obvious winner in a hypothetical samurai vs. ninja fight, as both have separate areas of expertise. Although Japanese samurai and ninjas share many common origins, there are many considerable differences between fighting styles and the equipment used during battle.
Ninjas begin to make an appearance in the 15th century and are commonly regarded as low-class mercenary assassins who are skilled more in the arts of deception and surprise rather than traditional combat. Ninjas wear a traditional, head-covering yoroi that allows maximum mobility in the battlefield, whereas a samurai warrior opted for a hefty suit of armor crafted from metals and carried swords and bows. Honorable and ancient, the samurai have roots dating as far back as 794 A.D. and are known for their code of honor, referred to as Bushido.