The film starts with Simon Spier (Nick Robinson) as he tells us about himself. His parents are former quarterback Jack (Josh Duhamel) and valedictorian Emily (Jennifer Garner). His younger sister Nora (Talitha Bateman) is an aspiring chef. Simon spends time with his three best friends - Leah (Katherine Langford), Nick (Jorge Lindeborg, Jr.), and Abby (Alexandra Shipp). He considers himself fairly normal, other than his one "huge-ass secret": he's gay. Before he heads to school, Simon sees a man he finds attractive working with a leaf blower. He tries to talk to him but ends up being awkward.
Simon picks his friends up for school. The only openly gay student at school is Ethan (Clark Moore), who is picked on by the school's resident jackasses Aaron (Tyler Chase) and Spencer (Terayle Hill). Their principal Mr. Worth (Tony Hale) always tries to relate to his students and always swipes students' phones for texting. Simon and Abby are performing in the school's production of "Cabaret", and their teacher, Ms. Albright (Natasha Rothwell) is frequently fed up with her students' lack of actual talent.
At home, Simon is watching TV with his family when Jack makes an unfortunate joke about a guy on "The Bachelor" looking "fruity". Later, Simon gets a FaceTime call from Leah, who tells him about the school's blog where an anonymous student going by "Blue" has come out as gay. Simon decides to start e-mailing Blue under the alias of "Jacques" (as in "Jacques a dit", which is French for "Simon says"). Blue responds to Simon, and the two continue sending each other messages and forming a strong connection.
Simon is at the school library where he accidentally leaves his e-mails open. They are found by his classmate Martin (Logan Miller), who has a reputation for being extremely weird and annoying. Martin approaches Simon and reveals he took screenshots of his e-mails and is effectively blackmailing Simon to set him up with Abby. Simon is upset but also isn't ready for everyone to know he's gay, so he reluctantly goes along with it.
At lunch, Simon's friend Bram (Keiynan Lonsdale) invites everyone to his house for a Halloween party. Simon starts to suspect that Bram could be Blue, based on their interactions and hints dropped in the e-mails.
Simon and his friends meet up at his house, where he and Leah are dressed as John Lennon and Yoko Ono, Nick is Cristiano Ronaldo, and Abby is Wonder Woman. He invites Martin, to the chagrin of his friends. On their way to the party, Martin ends up trying WAY too hard to talk to Abby, and she is clearly more interested in Nick. At the party, Nick tells Simon he is thinking of asking Abby out, but Simon comes up with a lie that Abby is seeing an older college guy. Simon is then invited by Bram to play beer pong and gets Martin and Abby to play against them. Simon later goes upstairs to find Bram making out with another girl, to Simon's disappointment. To make things worse, Martin blows chunks on Simon after getting too drunk.
Leah walks Simon back home as he wears her cardigan. They go to his room where Leah talks about loving one person for the rest of her life, meaning Simon himself. He doesn't get it and instead just goes to bed, and she sleeps on the floor.
Martin urges Simon to move faster with Abby, or else the e-mails get leaked. Simon gets Abby and Martin to go with him to rehearse lines for the play at a Waffle House. Martin tries to engage in conversation with Abby, who is anything but interested. He prods her for information regarding her move to Georgia from DC, which she ultimately admits is attributed to her parents' divorce and her father being a cheating jerk. Meanwhile, Simon becomes attracted to their waiter, Lyle (Joey Pollari), who Simon now believes could be Blue. Martin then tries to get Abby to say her name and say she deserves a "goddamn superhero". Martin goes as far as to get the attention of everyone in the restaurant until Abby says it, which she does so he'll shut up. Simon walks outside as Lyle is sending a message on his phone. They chat briefly until Lyle goes back inside, and Simon gets a message from Blue, who is planning to come out to his father.
Simon later takes Abby home and comes out to her. She says she is not surprised, even though she never suspected it, but she still loves Simon.
Martin starts hanging around Simon and his friends, but is closest to Abby (whether she likes it or not). This bothers Nick, who still wants to ask Abby out. Simon tells him that Leah has a crush on him and that he should ask her out instead.
The students go to their homecoming game. Simon sees Lyle and chats with him, but learns that he's straight and interested in Abby. As Simon walks away, he's approached by Martin, who's the school mascot. He asks Simon if he should make a romantic gesture for Abby, to which an apathetic Simon responds "Go big or go home". Martin uses this as an opportunity to pull a Kanye and interrupt the National Anthem so that he can ask Abby out in front of the entire school. Embarrassed, she gently tells him that she's just not into him like that. Martin walks away, humiliated.
Over Christmas break, Simon tries to call Martin to see if he's okay. Leah then calls Simon to tell him to go on the confession blog. Martin, trying to throw attention away from his homecoming debacle, ultimately posts Simon's e-mails, outing him. Nora sees the post and asks Simon, but he coldly turns her away.
Simon goes absent from his friends during the break. He comes out to his parents on Christmas, and they appear okay with it, but Jack makes another bad joke, and he and Simon don't speak for a while. To make things worse, Simon speaks to Blue one more time, and Blue chooses not to continue sending messages.
Simon spots his friends on the street. He goes to talk to them, but Nick and Abby are mad at him for making up lies to keep them apart. Simon admits what was going on with Martin and he apologizes, but they leave. Leah also admits to Simon that she was in love with him and would have been fine with him being gay, but she is still mad about the lying.
Upon returning to school, the other students all gawk at Simon after what happened. He approaches a student from his drama class, Cal (Miles Heizer), who Simon thought may have been Blue, but Cal denies it. During lunch, Simon sits alone when Aaron and Spencer call out him and Ethan and mock them in front of the cafeteria. Ms. Albright steps in and amazingly shuts the two bullies down and sends them to the principal's office. Simon and Ethan are forced to go as well so the boys can apologize to them. Simon talks to Ethan, who says that although he is open and confident about his homosexuality, it isn't at all easy for him, and his mother still pretends for the rest of his family that he is straight. Afterwards, Simon is going home when he is approached by Martin, who is very apologetic, but Simon tells him to fuck off.
Simon talks to his mom, who has no problem with him being gay and says he should be free to be himself. He later talks to his dad, who apologizes for all the times he's made dumb jokes, and he lets Simon know how much he loves him. Simon then helps Jack come up with a good slideshow for his and Emily's 20th anniversary.
Simon finds Leah walking her dog on the street. He apologizes to her for lying and admits that he has fallen in love with Blue. She forgives him and asks to know more about Blue.
Simon then posts a confession to the blog where he accepts himself and also apologizes to those that he hurt. Just about all of his classmates and teachers read it. He adds an invitation for Blue to find him somewhere after the school's play. The students at school now have a greater respect for Simon.
The school puts on its production of "Cabaret", which goes mostly well until the T on the sign breaks. After the show, Simon's friends (including Nick and Abby, who forgave him and are now dating) invite him to go with them to the carnival. Simon takes his entire stash of tickets and uses it to ride the ferris wheel in case Blue shows up. All of his friends and classmates stand by to see if he will arrive. After a while, it appears hopeless, but Martin shows up and tries to make it up to Simon. First he pretends he was Blue, but admits that's not true, and he gives the ride operator a few extra bucks to keep it going. Just then, Blue finally arrives, and it turns out to be...BRAM! Simon realizes who he is, and Bram admits that what he saw at the party was a drunk moment that ended quickly. When they reach the top, Simon and Bram kiss, and everyone cheers.
Later on, Simon picks up his friends from school, now including Bram, as they have begun dating. As they ride to school, Simon notes that it's a beautiful day and they should go on an adventure. His friends agree.
Simon Spier is a closeted gay high school student who begins an online correspondence with an anonymous gay student calling himself "Blue". Their e-mails are discovered by Simon's irritating classmate Martin, who blackmails Simon into hooking him up with his friend Abby. Simon reluctantly agrees, causing a rift between his best friends as he continues to lie to save his own back.
After Martin makes a failed and humiliating public attempt to ask Abby out, he impulsively leaks Simon's e-mails to the school's confession blog, effectively outing Simon. He then comes out to his parents on Christmas. Simon's mom is fine while his dad takes some time to talk to Simon about it, but they both love and support him. However, his friends become upset after learning about his lies, and Blue stops talking to Simon.
Simon later posts to the blog and becomes more open about who he is and that he can accept himself. Simon makes up with his friends and goes to the carnival where he waits for Blue on the ferris wheel. After a while, Blue arrives and turns out to be Simon's friend Bram. The two start to date afterwards.