In order to answer the question, it is essential to define what is a soul.
Yesterday, I was talking with a person who told me that Yom Kippur starts at sunset, and between the explanations given, it was required to "afflict their souls" and for this reason fasting was mandatory.
"What fasting has to do with "afflicting your soul?" I asked, "and when fasting, which one are you afflicting, your stomach or your desire to eat?"
So, as no credible respond was given, I decided to look by myself the definition of soul, and between the many web pages describing what a soul is, I think that this web page in one of the more accurate to define it.
I'm providing this link, because reading this topic it appears that many of the participants might have a misunderstanding of what soul means in religious terms.
I think, that after defining properly what a soul is, from a religious point of view an atheist definitively has a soul. So, regardless of the personal opinion or belief of the person, it has a soul according to religion.
From the atheist point of view, where religion is not a valid subject, an atheist can declare that he doesn't have one.