In her Remarks Upon Some Writers (1743), Catharine Trotter Cockburn takes a seemingly radical stance by asserting that it is possible for atheists to be virtuous. In this paper, I examine whether or not Cockburn’s views concerning atheism commit her to a naturalistic ethics and a so-called radical enlightenment position on the independence of morality and religion. First, I examine her response to William Warburton’s critique of Pierre Bayle’s arguments concerning the possibility of a society of virtuous atheists. I argue that this response shows Cockburn vacillating between a moral naturalism, on the one hand, and a theistic morality, on the other. Second, I draw on Cockburn’s letters to her niece, Ann Arbuthnot, and her opinions concerning mystical ideas about “the will of God” in north-east Scotland in the mid-eighteenth century. I maintain that these letters give us a fuller appreciation of Cockburn’s naturalistic position. My conclusion is that Cockburn’s ideas concerning atheism prompt us to consider the close interplay between secular and religious principles in so-called radical ideas of the period.