The phrase is made up of ninja, a much-revered warrior caste famed for their speed and agility, and edit, the process of changing a creative work.
The usefulness of ninja edits is typically hightened by bulletin boards that allow free editing of a post before any responses have been made, but make a mandatory note of any edits made after the first response has been made. Hence, if the author identifies the mistake, he or she must act quickly to rectify it before another poster replies.
Hey! I had a really fun day today, I went to the beach with my boyfriend.
Y reads the original post.
X then edits the post to read:
Hey! I had a really fun day today, I went to the beach with my girlfriend.
Meanwhile, Y has written, and subsequently entered, the post:
HAHA! You have a boyfriend? j00r a fag!
Y then reads the edited original post, then enters the post:
Oh! Nice ninja edit!
In this case, the thread would read, to a party reading it at a later time:
X: Hey! I had a really fun day today, I went to the beach with my girlfriend.
Y: HAHA! You have a boyfriend? j00r a fag!
Y: Oh! Nice ninja edit!