Invisiblity

[Jeff Clem]

Invisible creatures are visually undetectable. An invisible creature gains a +2 bonus on attack rolls against sighted opponents, and ignores its opponents' Dexterity bonuses to AC (if any). See the invisibility special ability.
Would this be considered being flat footed and would a Ninja be able to add his sneak attack dice to the attack?

[Cheapy]

Ninjas get their sneak attack damage when the enemy is denied its Dexterity bonus to AC.

Flat-footed happens to do that, as does invisibility.

[blackbloodtroll]

Yes.

[Castarr4]

It does not count as flat-footed. The target is simply denied their dexterity bonus to AC. That means that you use the "flat-footed" AC value, but they aren't actually flat-footed.

Luckily, your ninja only requires that they be denied their dex bonus, not the actual flat-footed condition:

SRD wrote:

The ninja’s attacks deal extra damage anytime her target would be denied a Dexterity bonus to AC (whether the target actually has a Dexterity bonus or not), or when the ninja flanks her target.

[blackbloodtroll]

I meant the sneak attack.