The pair puckered up for a same-sex smooch during the film, which tells the story of the 1970s rock group fronted by Joan Jett, played by Stewart, and Cherie Currie, played by Fanning.
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And Stewart, 19, admits she was restricted by working practice regulations when they filmed the kiss, because Fanning was so young.
She tells Access Hollywood, "She was 15, and I wasn't allowed to grope her. I'm actually not kidding, there are major restrictions that I don't remember (from) when I was younger."
She then stopped herself from spoiling the plot, adding: "I don't want to give anything way. It's a really passionate, hardcore scene ... It's just something that happened in their lives."
"The Runaways" hits theaters April 9.