Bilson, 39, posted the image back in early 2019, when Malek, 39, was positioned to and later won his first Oscar for his role as Freddie Mercury in Bohemian Rhapsody.
"Rami was a good friend of mine. We were in the same crew," Bilson shared of Malek during an appearance on Dax Shepard's Armchair Expert podcast. "We did The Crucible together senior year. We were the leads in it... He's always been extremely talented, really an amazing actor, even in high school."
The O.C. actress described the throwback shot of herself with Malek on a school trip as "the dorkiest picture of both of us," but said that the Mr. Robot actor didn't find the post to be particularly funny.
"I don't usually check my DMs on my Instagram and maybe a week goes by, and I actually look and I have a message from Rami," Bilson shared. "But it wasn't like, 'Hey! How are you?' It was straight to, 'I would really appreciate if you take that down. I'm a really private person.'"
Bilson was embarrassed by her former classmate's response, adding, "I was like oh, s**t, OK. Like, I get really hot, I start sweating, and I'm all nervous. I'm like, 'Oh my god, what did I do?'"
She added that it was less that Malek was in the photo with her and more of the actual image of the actor.
"I guess he didn't like the picture of himself, and I'm friends with his stylist and she was like, 'Well, it's not a great picture of him.' And I was like, 'OK, I'm sorry.' We were 16!" she said.
Bilson noted that her O.C. producer pal, Josh Schwartz, told her "You did him dirty" and she said she felt as if she'd posted a controversial image of Malek instead of a fun throwback pic.
"I removed it, and I even wrote to him a really nice message like, 'I'm so sorry! Go get the Oscar! You're doing amazing.' And I never heard anything back, which is fine," she said. "I was super bummed because he was so nice, and we were good friends. I'm a big fan of not taking yourself seriously, especially at that level of fame and talent. But look, he wants to be super respected. It's his thing, so I respected it. I took it down. I was just a little bummed at how it was handled."