The 42-year-old "Bang Bang" star took to Twitter to share his response.
"There are more chances of me having had an affair with the Pope then any of the (I'm sure wonderful) women the media has been naming. Thanks but no thanks," Hrithik posted.
There were rumours that Hrithik and Kangana dated though the duo never publicly acknowledged the relationship. Kangana and Hrithik have worked together in "Kites" and "Krrish 3".