Simon Spier is a 16-year-old high school junior with what appears to be a perfect life: loving parents, an awesome younger sister and cool older sister, and his three best friends, Nick, Abby, and Leah. Unbeknownst to his family and friends, however, Simon is hiding the fact that he's gay. One day, he learns through his school's confession website that there is one other gay student at his Georgia high school. The two begin emailing each other under codenames -- the mystery student is Blue, and Simon goes by Jacques, referencing "Jacques-a-dit", the French for "Simon Says." Simon finds himself falling in love with Blue, who shares his love for Oreos and his fear of coming out, but Blue is uncomfortable to reveal himself to Simon.
Disaster strikes when Martin, one of Simon's classmates, stumbles upon these email communications and uses them to blackmail Simon into helping him get a date with Simon's friend, Abby. Simon reluctantly agrees in order to protect Blue's secret, inviting Martin to hang out with Abby at anytime. Abby isn't interested, as she's falling for Nick. Leah, however, seems to be falling for Nick in Simon's mind.
As time passes, Simon wonders about who Blue could be, suspecting boys like Cal Price, the stage manager of the school play, soccer player Bram Greenfeld, and even Martin playing a cruel trick. The group, without Leah, goes to a gay restaurant for Simon and faces the wrath of Simon's parents when he comes home drunk. Simon comes out to Abby and is relieved when she takes it well. Things go sour when Martin and Simon argue, and Martin retaliates by outing him on the school's confession site. Simon becomes the subject of harsh bullying at school, and Leah gets upset at him, feeling betrayed that he didn't tell her. He comes out to his parents, who thankfully accept him.
After the last performance of the school musical, Simon goes to the carnival and waits for Blue on the Tilt-A-Whirl It turns out to be Bram Greenfeld, the cute soccer player he thought was interested in Leah. The two ride the ride together and decide to date the next day at school. Simon reconciles with his friends and the group meets up with Bram and Garrett as they watch Abby and Leah perform at the talent show.