This rules out my example, but I am giving it anyway, darn it. In *A Taste for Death *by Peter O’Donnell, Modesty Blaise fences against an evil fencing master who out-classes her technically–but of course Modesty is better in a fight to the death.
In the short story Rogues in the House, Conan is hired by (and teams up with) a nobleman named Murilo who is an expert swordsman. In the comics adaptation, I seem to recall there being something about Murilo giving Conan a few pointers (hah!) on swordplay, but I don’t know if it was in the original story. In any case, Murilo wasn’t a teacher of any sort that I know of, and he wasn’t the bad guy, either.
(To refresh your memory on the plot: Murilo hires Conan to kill Nabonidas the Red Priest or whatever he’s called, arranges for Conan to be sprung from prison, that gets botched but Conan escapes anyway BECAUSE HE’S CONAN, Conan decides to follow through on the job, finds Murilo and Nabby being held hostage by the intelligent ape named Thak, and fighting ensues.)
There’s a similar scene in one of the Honor Harrington books, by David Weber (I think it was Flag in Exile). She won because, as she puts it, she’s been there before (that is, in a kill-or-be-killed fight). Never mind that most of her previous fights were from the bridge of a starship.
And in a later book, she easily defeats a professional duelist in her first duel (with pistols). So I guess being there before is overrated.
The ‘Space Marines’ do hand to hand combat, but she wasn’t a marine. She did do coup de vitesse, some funky futuristic corm of martial art [I seem to remember it combined karate, judo and savate or something like that] and she did the full contact style of practice.
But you are right, she didn’t normally fight with anything smaller than a cutter.
I suppose that technically, a katana is a cutter. 
And she was actually in a human-scale fight to the death earlier in the same book, though I’d still think that a silver platter improvised as a discus is rather different from a sword.
You can probably guess that the protagonist of KJ Parker’s Fencer trilogy is a fencing master.
*Spoilers! *Geez!
Count Dooku from the Star Wars prequels used the Makashi lightsaber form, which is more or less fencing.
I wouldn’t consider hand to hand duking it out with an occasional thrown object the same as fencing master. That was desperation as the bad guys slipped in an assassination squad disguiesd as security personnel with a message delivery. Her duel against the professional duelist [who did occasionally use sword if that is what the designated victim wanted] was hand guns [10 mm dueling pistols gunpowder type]
I still think the Fencing Master from The Benignity of the Compassionate Hand qualifies the best as he was deliberately sent to assassinate someone.
There was a duel in The Deed of Paksennarrian also by Elizabeth Moon, but it was a disgruntled ex-mercenary troop member. She wasn’t an actual assassin, just being used to target the Duke and Paks.
Sir Ravenhurst in The Court Jester
Baron Rolfe Von Stuppe in The Great Race
In the War of Powers novels (Vardeman, Robert E. & Milan, Victor, 1980) one of the antagonists is Prince Rann, cousin to the love interest (the antagonist/protagonist Princess Moriana). Rann is a sadist, but is possibly the greatest swordsman in the Sundered Realm.
In the final battle with the Fallen Ones, the protagonist Fost and Rann are forced to fight together, and Fost comments that Rann did not parry in the fight - every move was an attacking one, such was his skill. Inevitably, though, Rann is mortally wounded as they make their escape having saved the realm (Fost is much more pragmatic and always aims to survive).
The Star Trek novel Shadow Lord was set on a distant planet with an alien species that used swords. They had very ritualized combat. The protagonist is a young prince, his antogonist is IIRC his older brother, who is much better with a sword. They end up having a duel. Fortunately, Sulu was around.
Then there’s a movie, By the Sword, starring Eric Roberts. He plays the fencing master a fencing school, and gets into conflict with the main character. But it isn’t fantasy or SF.
The evil fencing master is unusual, but the evil/morally ambivalent top blade is common. In the Muirwood books, Count Dieyre was acknowledged as the best blade of his generation. I can’t recall if Colvin ever actually fought him, as he always dreaded doing.
I don’t know if I’d call the guy evil but in the last book of the Amber series, Corwin killed his son’s fencing master on the shores of chaos by cheating in a throwaway scene. I liked Zelazny for fight scenes, as he was a fencer himself and gave a bit more detail.
And to correct everyone: the evil fencing master in “Die Another Day” was Madonna. Pike and Pearce were the products of her tutelage.
Tim Roth’s character in Rob Roy is most definitely a fencing master, and most definitely evil.
Does Darth Vader or Count Dooku count?
They might be expert fencers, but I’m guessing a better fit as per the OP is that saber-wielding mentor who painstakingly trains our hero on the finer points of parrying with Dear Old Dad’s sword while making sure to explain that, oh, hey, by the way, just so you know: the Black Knight murdered your father.
And so Luke eventually goes off to have a swordfight with the designated target – Obi-Wan has taught you well! – thanks to said scum-o lie.
THE AVENGERS – with the Norse gods and the dude in power armor and the hulking guy mutated by radiation – repeatedly featured the world’s greatest swordsman, a professional criminal who loved (a) passing himself off as a superhero, and (b) taunting Hawkeye as the weaponry expert’s villainous former mentor. So in his first appearance, we get the obligatory flashback (“Keep practicin’, kid! We’re gonna make a great team! But never forget which one of us is the master!” … “You didn’t think I wasted all that time teachin’ you for my health, did you? This is what I always planned!”) to later set up issue after issue of the guy’s signature schtick:
“We are old ‘friends’, Natasha! I taught him all he knows!”
“A good maneuver, Hawkeye! But unfortunately for you, you’re up against your master!”
“You are an apt pupil, indeed! But never forget . . . it’s the Swordsman who is the master!”
(“The Swordsman always considered himself my master . . . since he taught me my skills years ago in our carnival days!”)
“I thought I had taught you the danger of overconfidence years ago! But, at any rate, your reflexes are swift enough . . . !”
“Had you not turned against me, I might be proud of your progress, Hawkeye! You have proven to be a worthy student of the sensational Swordsman!”
Wow. Yoda spent months training and feeding the kid on Dagobah in some Force-forsaken swamp and who gets all the credit? Some guy who gave him one half-assed lesson against a hover drone before he died.