"The child-pope Benedict IX (who became Pope at the age of 12!) was bi-sexual, sodomised animals, ordered murders and dabbled in witchcraft and Satanism. He loved to throw wild, bi-sexual orgies. Benedict IX held the post of Pope in the years 1032-44, 1045 and 1047-48. He was described as "A demon from hell in the disguise of a priest...", and St Peter Damian said of him: "That wretch, from the beginning of his pontificate to the end of his life, feasted on immorality". Dante estimated that under Benedict IX the papacy reached an all-time low in immorality and debauchery. When he was 23 he survived an assassination attempt (strangling at the altar during Mass). Benedict went on to marry his cousin and sell the papacy to his godfather, Gregory VI."
but it doesn't mention is atheism or otherwise. We have to assume he was a good Christian, perhaps with the occasional lapse into Satanism (after all no one is infallible). I note the present Pope has chosen the name Benedict, could be that he hopes to emulate....no better not go there.
Here's a better candidate:
"It was widely rumoured that the ex-pirate Pope John XXIII (1410-15) was an Atheist. He tortured his own cardinals and was said to have "had wicked company with two of his own sisters". Robert Hallum, Bishop of Salisbury said that he: "ought to be burnt at the stake"."
for more naughty popes see
http://www.geocities.com/missus_gumby/papal.htm