In a new interview for V magazine's Summer Hollywood issue, Theron, 40, revealed she had a "rough time" filming with Maguire on the 1999 film.
"Tobey and I had a bit of a rough time, yeah. I mean, we're good now. It was a difficult movie," she said. "Every day is completely different for a completely different reason. Whether it's the weather, or the writing isn't there, or you don't get along with your castmate you have to be able to go to something else that's just as powerful. Does it make it as enjoyable? Probably not."
She continued: "I mean, there were just a couple of days that Tobey and I had a rough time. The rest of the movie, we actually had a really good time."
But despite any tension behind the scenes, Theron said she's thankful for the experience and looks back at her time on set as a learning experience.
"I love Tobey. I'm kind of glad we had that experience on that movie," she said. "It teaches you different things. It taught me that I could fall in love with somebody in my head while looking at someone else. We had some really intimate moments. Tobey and I didn't feel that way about each other, so I had to figure something else out."
This isn't the first time Theron has admitted to butting heads with a fellow costar. She previously said she didn't get along with Tom Hardy while filming Mad Max: Fury Road.
"From what I hear, he's not like that on every movie – I hear he's had good experiences," Theron said of working with Hardy. "Maybe the movie is what it is because we struggled so much with each other, and those characters had to struggle so much with each other. If we were chum-chum, maybe the movie would have been 10 times worse."