I am looking for a fantasy story preferably LitRPG but with a smart MC, Not necessarily a genius but that is difficult to deceive

You can try mine ^^
The MC is not smart, but he tries to question things and learn from his mistakes. ;)

>tfw too smart to be fantasy story protagonist

Well, if already some people are doing self-advertising, I'll just join them shamelessly. My fiction "I hate being wed in a fantasy world!" sports a protagonist, who's smart in many areas.

Kidnapped into a fantasy world, equipped with a system like an RPG, he figures out the game-stuff which can be put into effect, and what doesn't, while he stays vigilant and asks a lot of questions about his situation. He's not easily deceived, though this may be because he suspects about everything (especially at the start).

Though he has a lot of shortcomings, he's the kind of MC, who embodies some intelligence, cleverness, and resourcefulness, while being hindered by his flaws and choices.

This is a rather wide range of fictions that could be recommendede, but maybe A Hero's War by jseah would fit.  It is active, has over 100 chapters, updates are quite slow atm.

I don't know if you want a generally intelligent MC or if it has to be a crafty, scheming MC, the one in this fiction is intelligent, but quite honest.

http://royalroadl.com/fiction/2826/a-heros-war

A Hero's War is a fantasy story, about people being transported into a different world, no LitRPG. There is Mory, who was summoned by the queen, hailed as a hero and sent on a quest to find a legendary sword to save the people from monsters (a side character in this story). Then there is Cato, who just woke up in a forest full of monsters in a different world, not knowing how he got there. He goes on  a journey to find out about the world, reinvent earths technology and research magic. Another goal of his is to bring an industrial revolution, empowering the commoners through the rise of technology and education.

So MC is intelligent when i comes to technical stuff, research, but also how to start his businesses, how to gain support from a noble, how to change society and has proven that he can also scheme a little bit to achieve his goals (like the spread of knowledge that the nobles want to keep secret).

wake of the ravager I think would be a good one. He starts off being dumb but as he upgrades his stats he turns kinda genius. What also helps is that the mc has a modern person from our time in his head (he lives in a medieval era style world)

Well, I'm writing this one, and it does have a smart mc. Not like Code Geass smart, but adequately smart, and it is a fantasy novel:



Shima Akio is mysteriously reborn in the game world of Divinity, only, it is no longer a game. Watch as Akio, now called Jon in the new world, grows stronger to be able to face stronger foes and protect his new family, while uncovering the mysteries behind his reincarnation, and thus finding the truth about this world...

My central protagonist Jian Cheng is a conniving schemer who is shameless but driven to improve and protect his friends and family at all costs. Fatty Li Feng is flawed but clever too. Li Feng is ... Enthusiastic...

BLURB:

Three young friends try to make their way together, through the dog-eat-dog cultivation world of the jianghu -- and even worse, their teens!.
They have chosen to take the path less travelled, by rising as a single entity -- of three entirely separate individual people -- The Thundering Tortoise Trio!


Along their merry, yet sometimes scary, way, Jian Cheng, Fatty Li Feng and Fairy Fen Ling will forsake their own petty selfishness, their hateful overbearing sect, conventional cultivation wisdom and even the entire righteous path, for the family they have become... And for benefits of course!
After all, everyone loves benefits!
Join these three friends with benefits (*we're not changing the title though...), as they probably overcome every obstacle (* but no promises) to bravely forge their own future!

https://www.royalroad.com/fiction/27613/the-thundering-tortoise-trio

The characters from my story are pretty smart, as it is about how politics and war go hand-in-hand.
I would also recommend Dauntless, a Code Geass story from Fanfiction.net, super intelligent. Or Embers, an Avatar Last Airbender story from fanfiction.net.

The Metropolitan Man (a Superman reinterpretation in the point of view of Lex Luthor) is probably the single best fan fiction ever written and an excellent example of a smart main character in a fantasy story. Also it's written by Alexander Wales who does Worth the Candle, so there's that.

Here's a short little list!

Foreststorm
A very smart mc!
"Ves'ra is born in a small tribe of kobolds in the middle of a huge forest. She is happy with her life until several members of her tribe start disappearing. She sets out on a journey to find those responsible."

The Demononologues
Mc is pretty dang smart, but also goofy and likes to have fun.
"Indigo woke up in a body she didn't recognize, and a world she didn't know, without memories or even a name to define herself.
Follow her life as she discovers that, not everything happens for a reason, not all bad guys are out to conquer the world, and being powerful doesn't automatically make life easy.
Follow her adventures as she gets drunk with orcs, raids ruins for lost treasure, and chops the heads off hordes of zombies.
Follow her journeys as she meets people, makes friends, and does her best not to kill everyone around her."


Katalepsis
A decently smart mc when she gets going, but the rest of the cast really work their brain magic!
"Nightmares and hallucinations have plagued Heather Morell all her life.
 
Diagnosed with schizophrenia as a child after the loss of her twin – a sister who never really existed – now struggling with her mental health at university, Heather teeters on the verge of giving up on life. A chance meeting ends in a revelation: she is not crazy, her visions are all too real, and probably want to eat her soul.
Embroiled with a crippled, bad-tempered magician and her self-proclaimed ‘bodyguard’, Heather rapidly descends into a world of terrifying magic and otherworldly monsters, in an effort to stay sane, bring back the dead, and maybe, just maybe, make out with cool older girls."


Eight
Experience breeds wisdom, and this old(young) man is chock full of it and with an abundance of knowledge to boot!
"His name is Eight. Not really, but that’s what the System decided after a slip of the tongue. One moment, he was stepping out the office door on the way home, and the next waking up on a hillside below a town wall. Oh, and the gate guard drove him off, because he thought Eight was a monster.

Life’s tough when you’re trapped in an eight-year old body on another world."

Fantasia
Mc is smart and also a tiny bit dense
"Arwyn has just bought Fantasia, the first fantasy-based VRMMORPG, with 99% realism that you can play while you sleep. In the game, she becomes Fey, a moon elf starting in the magical Elvenwood. Join her (and her snarky narrator who likes to interject sarcastic comments in parentheses) on her exciting, often hilarious adventures inside this magical world full of every fantasy creature you've ever encountered in books, games, and movies, and a few that you haven't.

Oh, and there's something strange about the NPCs in this game... See if you can figure it out before Fey does. (No, they are not self-aware AIs.)"

The Guild Chronicles
Mc is very smart and extremely competent.
"With an indifferent king and an imbalance of wealth, the lives of commoners are never easy. Especially now that abductions are on the rise, villages are being attacked, and monsters are on the loose. As a member of The Guild, a militant grassroots organization, Bronwyn's task is clear. Save the people and destroy the monsters. The only question is if she will rise to the occasion, or will the monsters in the countryside- and those of her past- cut her down?"

Empire of Salt
Mc is very smart, but not power hungry, its a fun combo!
"I just wanted to live my second life like I remembered my first, unbothered by the petty squabbles of the rich and powerful.
Sadly life, and other humans don't care about one's dreams, so I'll have to make due.
How do I plan to get back at them?
Well, it all starts with a bucket of saltwater."

An Advance In Time

In the year 2050, nanotech was invented that allowed humanity to do what it does best: ignore reality. Jason was a project manager at Razor, Inc. where those simulations were crafted and improved every day.  
That is, until an accident with a power outage and a poorly-coded backup protocol saw his consciousness transferred to a server and his body in a coma for the foreseeable future. 
With the corporate vultures circling around what they see as a new piece of company software, Jason ultimately found himself in one of the simulations he used to work on with a new set of objectives:  
1. Survive the medieval setting  
2. Build a Kingdom from scratch before ten years are up and end the scenario
3. Prove to the rest of the world, who will be watching him closely, that he’s not going to be a crazy human / AI hybrid that would take over the world if given half the chance.  
4. Figure out how #2 and #3 are compatible...
His modern knowledge of technology, chemistry, and physics is a huge advantage, but he wants to reinvent centuries worth of advancement in a few short years and innovate like his life depends on it. Because soon, it will.  
If you enjoy kingdom-building, strategy, technological progression and big challenges, you’ll likely enjoy An Advance In Time.
Remember to follow the story by clicking the bookmark icon and add the story to your favorites list!  
Reader comments:
“It’s like those incremental games, but much much more entertaining. I can’t wait to see where this goes, and can’t wait for the next update!” - Reddit user
“Solid prose and an interesting start... I’m always a sucker for industrialization, so I think I’ll be watching this.” - Reddit user
“The story is just the type of story I love reading.” -RoyalRoad reviewer  
[participant in the Royal Road Writathon challenge]

i'd recommend Dungeon Defense.