As far as I know, a great history of atheism has yet to be written, but to my knowledge we have no record of actual medieval atheists. We have authorities who occasionally call people atheists, but in general there's little evidence that these people were atheists rather than other kinds of heretics. Clerical demonizations of opponents at times took on the form of an almost standardized litany, with persecutors just heaping on the accusations against the persecuted.

"Modern atheism" is often traced to people like Jean Meslier, writing in the 18th century or Baruch Spinoza in the 17th century or Giordano Bruno writing in there 16th. Often times, with these early atheists or proto-atheists, it's difficult to understand and disentangle whether they're "deists"/"pantheists"/"free thinkers" or truly deny any sort of transcendent supernatural reality as modern atheists do. That is, those firmly against organized religion but open to the idea of some superhuman power and those who reject it all. During this period, historians are often forced to talk about such-and-such's "alleged atheism". I tend to come down on the side that most to all of these thinkers were not atheist in the modern sense (perhaps "deist" is a good catch all term), but many other come down on the other side, arguing that these men were atheists but made careful public statements and never pushed the envelope too far because of fear of persecution. I tend to think that modern atheists tend to overemphasize how "rational" and "natural" atheism is, in the sense that it's a pretty radical break from a long tradition where even rational philosophy and science ("natural philosophy") was rooted in belief in God, a divinely ordered world, etc. The sort of assumptions that people have and the language they used can make it difficult to distinguish between "pantheists" and "atheists".

But in short, if there were modern-style atheists rather, they left no record for us. And if we expand our circle slightly to include pantheists and free thinkers (who really get their start, as far as I know, towards the end of the 16th century, in part because the Protestant Reformation has began calling into question and reopening all sorts of doctrinal questions and new printing technology let ideas spread like never before), many of the early ones are killed by both Catholics and Protestants.