In the Islamic world, there were people who questioned at least the Islamic conception of religion. The most famous was Ibn al-Rawandi (827-911AD), who started out as a Sunni, then became a Shi'ite, and eventually rejected all forms of revealed religion, and wrote a book called The Book of the Emerald which attacked Islam and various parts of the Qu'ran, and how it and the Bible contradicted each other. However, as we don't have his book, only references in other books, we don't actually know if he actually actively believed in no God, or was simply sceptical of the particular religions he encountered. Ie was he actually an atheist, or simply not a Muslim/Christian/Jew/etc. There's a couple of other famous Arab writers from the time who also attacked religion. It was a very rare occurence however.

In the Christian world, however? No. We have no sources espousing atheism or talking about people espousing atheism, except occasionally in very obviously propagandistic attacks on people's enemies (and even then, they don't tend to actually say their enemy did not believe in God, but rather that they did not believe in eternal life, or something like that). (It is of course, possible that there were medieval Europeans who secretly believed in their hearts that everyone around them was wrong and everything they'd ever been taught was a lie... but if they did, they didn't say it. And I doubt there'd be many.)

Depending on your definition of atheism, you might be able to argue that, say, some Chinese buddhists or taoists could be defined as atheists in the Middle Ages, but that's probably not really what you're thinking of, and I don't have the knowledge to really go into that.

I should add to this, that my answer is not intended to show that before the modern period there were no (or at least, a statistically insignificant number) of atheists. Simply that this was the case in the Middle Ages. They certainly existed in the Classical Era.