Most scholars dismiss this is as fiction. Indeed the Catholic Encyclopedia brings up multiple variations on the story, each of which can be easily debunked.
Perhaps the most damning proof that this is a legend would stem from the fact that nobody - including enemies at the time - ever made such accusations. From Wikipedia:
It is also notable that enemies of the papacy in the 9th century make no mention of a female pope. For example, Photios I of Constantinople, who became Patriarch in 858 and was deposed by Pope Nicholas I in 863, was an enemy of the pope. He vehemently asserted his own authority as patriarch over that of the pope in Rome, and would have made the most of any scandal of that time regarding the papacy; but he never mentions the story once in any of his voluminous writings. Indeed, at one point he mentions "Leo and Benedict, successively great priests of the Roman Church".
This book is a book dedicated entirely to dealing with all the variations on the story, and debunking each.