Flynn was in a relationship with "Game of Thrones" co-star Lena Headey; rumours spread about the relationship ending on bad terms some time before March 2014, resulting in the couple being kept apart on-set. However, Flynn rebuffed the claims, stating he and Headey had worked in a scene together, adding "And the last time I saw Lena we were speaking, so I wouldn’t believe everything you read, and like I said, media can get pretty desperate for stories." He continued by calling Headey "…a wonderful person and a wonderful actress."