Let's see. Some possibilities and notes.
1st, definitely need to get a silver weapon or two early on, as Reveille mentioned.
2nd, Ranger can work, with their Track feat, animal companion to help in tracking (get a canine or something else with Scent), and Favored Enemies (obviously, choosing Humanoid - Shapechanger at first, then choosing Giant as your second FE: humanoids and giants are the two kinds of creature that can become werewolves).
You might multiclass into Paladin, if you're Lawful Good, after gaining 5th-level as a Ranger for the second favored enemy. Werewolves are always Chaotic Evil, so a Paladin's Smite Evil and spells would be very effective against them. Paladins can Remove Disease, like lycanthropy, IIRC, to prevent new werewolf victims from turning into werewolves themselves.
You could just start as a Paladin, if you liked, but probably don't bother multiclassing if so. Clerics can also be effective, since they can Remove Disease as well and they can be effective in melee combat. Plus, they could take the Animal domain to be better at dealing with a werewolf's normal wolf minions, if any.
There's the Bloodhound prestige class, which appeared in Masters of the Wild for 3.0 D&D; it may've been reprinted in 3.5's Complete Warrior or Complete Adventurer, so check and see. It's an effective tracker and warrior, though it doesn't get any Favored Enemy increases for multiclassed Rangers, so it may or may not be good for you.
The Foehunter prestige class is absurdly powerful and broken, but it fits exactly the kind of idea you're going for. Of course, it's only absurdly powerful and broken when you face the chosen type of Hated Enemy; the rest of the time it's just below average. Foehunter is also in Masters of the Wild, so it may have been reprinted in 3.5's Complete Warrior or Complete Adventurer; I mean, they reprinted the Frenzied Berserker from MotW after all, against all reason and sanity, so why not?
The King of the Wild prestige class (primarily the King of the Forest or King of the Plains versions) is also fitting, and also comes from Masters of the Wild. I don't think it was ever reprinted in 3.5, because the 3.5 DMG's Horizon Walker prestige class is similar in concept but terribly mediocre in comparison. Kings of the Wild are fairly strong, but not quite broken, whereas Horizon Walkers are just average warriors that are ever-so-marginally better against foes from certain environments.