Most cooks didn't have access to any kind of precision timer, and in any case, timing in the medieval era was something of a movable feast (pun intended) - in some cases, as measured by certain monasteries, an hour in daytime in summer was longer than an hour of daytime in winter, and vice versa at night. Even in elite households, the idea of precise time measurement didn't really happen. See this excellent answer for some more information about time, which totally isn't my area: https://www.reddit.com/r/AskHistorians/comments/58ihsp/before_the_invention_of_clocks_or_at_least_before/d90vum0/

That said, there were some timing methods that could be relied upon, more or less. The time taken for a candle to burn a certain distance is pretty stable, assuming you have consistent wax and wicking, and the candle is not in a draft. So it might be reasonable for a cook in a household that could afford such thing to say "take that out when the candle reaches this mark". We've no written evidence of this in kitchens, as far as I'm aware, but the concept existed.

What we do have in written records - recipes, in this case - is instructions like "cook it until it is done", "cook it until it is brown", or "cook it until the beans are soft". To modern eyes, this is completely unhelpful, but it assumes that the cook has a certain level of experience and expertise, and that they know when a thing will be done. Since written recipes were only used in elite households, it's fair to assume that a cook who has access to one has that experience. However, there is the very occasional instruction to cook something for the length of time it takes to say a particular prayer twice.

Mostly, though, people who learned to cook would have learned timing as part of it. They might have had little mental tricks to help (when that shadow moves that far, take the bread out), or, more likely, just developed a good sense of time as part of the skill of cooking - even modern cooks do this, to some degree.

And then there's the point that medieval and indeed most pre-modern cookery just doesn't need precise timing in the same way some modern dishes do. Stews and pottages - the main elements of medieval cookery - take hours, but half an hour more once they're done won't hurt; it might even improve it. Some Arabic recipes essentially say "let the fire go out under it". Bread and pies were cooked in ovens where you could open the door and look, and not at temperatures where things would be quickly burnt - and pie fillings were often pre-cooked. Roasted meats, mostly the domain of the elite, are right in front of the cook to look at and prod and run skewers into to check.

And in addition to all of the above - precise timing isn't all it's cracked up to be in modern cookery. There are differences in ovens and hobs, and what takes exactly 7 minutes in one oven might take 6 in another, or 9. Knowing your equipment is a key aspect of cookery now, and that was just as true and more so in the middle ages.