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- One is needed for the quest The Only Cure.
- Inside of Mzinchaleft in a chest located atop the dwarven pipes located near a double stair-set just before you enter the Lever Maze to activate the valve.
- The Emperor's Quarters on The Katariah.
- Amaund Motierre carries one.
- Randomly found in urns/chests (With Prowler's Profit the chances are greatly increased).
- There is also a chance you could get one from Harrald Law-Giver who can be found in Riften next to the Mistveil Keep sparring with a dummy. He will give you a short quest upon speaking to him and the reward for the quest is two of any precious gems. These gems are random and can be changed simply by loading a previous existing save and requesting your reward again. Do this until you get a Flawless Ruby.
- One or even two may be found in Fahlbtharz, dropped by a Dwemer Sphere and/or in the large chest at the end of the Great Hall.
- One may be in a strong box on an unmarked island located southwest of Raven Rock.
- Under the word wall in the frozen lake at the Forgotten Vale.
- On a docked boat on the side of the river next to Kolskeggr Mine. Jump off the bridge infront of Pavo's House (at Kolskeggr Mine) onto the waterfall. Go down the waterfall and go right, this will lead you up the river. Go over the large patch of weeds, rocks and branches keep going down the river. The boat will be "docked" on the left side of the river. On the bottom of the boat there are several gems, regular and flawless. Under the boat there is a chest.
- Can be found as random loot on giants.
- If Dawnguard is installed, then a flawless ruby can be found just to the left of the Inner Sanctum in Forgotten Vale on a skeleton. This requires careful handling as the skeleton is located very close to the edge and they will fall off and into the valley if the wrong gem is picked up first.