Yes, it is an evil act - depending on what rule sources you use
The Core rules
In the core rulebook - copied directly from the 3.5 SRD - the rule on descriptors like [Evil] is:
Most of these descriptors have no game effect by themselves, but they govern how the spell interacts with other spells, with special abilities, with unusual creatures, with alignment, and so on.
In other words, with these rules, [Evil] spells just mean that they interact in specific ways with certain abilities (detect evil, a cleric's spellcasting restriction). Casting an evil spell may also be an evil act, and often is - but it isn't so automatically according to the core rules.
Animate dead is a bit of a grey area, and would depend a lot on the metaphycics of your game - I.E. "Ask your GM". Even in the most forgiving interpretation, it would raise questions about the desecration of remains.
Further rule clarifications
However, the game designers are of the opinion that casting an [Evil] spell is also an evil act. See for example this quite here:
Spells with the Evil descriptor are evil; that's why they have that descriptor. Same goes for Good or Lawful or Chaotic.
Furthermore, from what I can find this has been confirmed in later published rulebooks (Pathfinder Roleplaying Game: Horror Adventures), although I cannot confirm that as I do not have that book. (A second-source quote is found here, halfway in the "Descriptor" section).
It seems, then, that the designer intent (in Pathfinder) is that [Evil]-spells are, indeed, Evil acts, and depending on where you source your rules from, it might or might not be RAW.
An evil act does not make you evil
Characters should not be fully defined by one alignment - people can and do perform acts outside of their normal moral, for whatever reasons. Performing multiple evil acts will likely push your character towards being evil, but an "the ends justify the means"-mindset could very much keep you neutral.
Problems with the [Evil] being Evil interpretation
Most [Evil] spells are, in fact, always evil acts - creating permanent, intelligent undead (such as with create undead) can't really be justified away. For many others, however, it makes much less sense - casting Magic Circle against Evil (a [Good] spell) to trap a demon you summoned should hardly be considered a good act. However, a blanket application of the rules would make it so.