Melt the butter over medium heat in a medium saucepan. Add the onions. Cook, stirring often, until the onions are golden brown, about 10 minutes. Reduce the heat to medium-low if the onions are browning too fast. We don't want them burnt.
Mix the kosher salt, black pepper, and thyme into the flour and sprinkle the mixture into the pan, whisking it in. Cook the flour for 2 minutes.
Add the hot chicken stock and cognac. Cook uncovered, whisking occasionally, until thickened, for about 5 minutes. Taste and decide if you'd like to add more salt.
An optional step is to strain the onion for a smoother gravy. I usually do, but you can leave it in.
Serve the gravy immediately, or refrigerate it covered for up to 4 days.
Video
Notes
Gluten-free option: Skip the flour. After browning the onions, add the spices, hot chicken stock, and cognac. Bring to a gentle simmer, then whisk in a cornstarch slurry (1 tablespoon gluten-free cornstarch mixed with 2 tablespoons of cold water). Cook, stirring, just until it thickens, for about 1 minute. Remove from the heat immediately. Another option is to use gluten-free all-purpose flour, using it the same way you would use regular flour. It won't be as good, but it will be an effective thickener.
The recipe yields about one cup, or four servings, and can easily be doubled if you're cooking for a crowd.
While low-carb options to all-purpose flour exist, including coconut flour and konjac flour, I'm not a fan of them in this case. Flour-based gravies have a rich, full, velvety texture. Since I make this gravy for holiday meals and not as an everyday occurrence, I prefer to go the classic route and use a smaller quantity of the real thing.
I usually add ¼ teaspoon of Diamond Crystal Kosher Salt, which is equivalent to ⅛ teaspoon of any other salt (including Morton kosher salt). However, since I recommend using salted chicken stock and salted butter, you might find that there's no need for added salt. So, you might want to skip the salt, taste the gravy when it's done, and decide if you'd like to add salt to taste.
Leftover gravy keeps and reheats well. You can store it in an airtight container in the fridge for up to four days, or freeze it for up to three months in freezer-safe containers, leaving space for expansion. When reheating, gently warm it on the stovetop over medium-low heat, stirring frequently, or use the microwave in short intervals, stirring after each session. If the gravy has thickened too much while stored, whisk in 1-2 tablespoons of broth, water, or milk.