Ninja is the on'yomi reading of the two kanji "忍者". In the native kun'yomi reading, it is read shinobi, a shortened form of the longer transcription shinobi-no-mono (忍の者). The term shinobi has been traced as far back as the late 8th century to poems in the Man'yōshū.[7][8] The underlying connotation of shinobi (忍) means "to steal away" and — by extension — "to forbear", hence its association with stealth and invisibility. Mono (者) means "a person".

Historically, the word ninja was not in common use, and a variety of regional colloquialisms evolved to describe what would later be dubbed ninjas. Along with shinobi, some examples include monomi ("one who sees"), nokizaru ("macaque on the roof"), rappa ("ruffian"), kusa ("grass") and Iga-mono ("one from Iga").[5] In historical documents, shinobi is almost always used.

Kunoichi, meaning a female ninja,[9] supposedly came from the characters くノ一 (pronounced ku, no and ichi), which make up the three strokes that form the kanji for "woman" (女).

In the West, the word ninja became more prevalent than shinobi in the post-World War II culture, possibly because it was more comfortable for Western speakers.[10] In English, the plural of ninja can be either unchanged as ninja, reflecting the Japanese language's lack of grammatical number, or the regular English plural ninjas.[11]