A Year of Secret Assignments tells the story of three private school girls who are forced to write letters to boys at a public high school with a bad reputation. Throughout this experience, all the students learn about expectations, honesty, and themselves.

Lydia, Emily and Cassie are three tenth grade girls at Ashbury High, a private high school in the suburbs of Sydney, Australia. As part of an English class assignment they must write letters to students at neighboring high school Brookfield, which has a terrible reputation. In addition to this assignment, as part of their long-lived friendship, Lydia periodically assigns Cassie and Emily secret missions (or "secret assignments") ranging from baking to shoplifting. The Pen Pal Project gets off to a bumpy start, with each girl unsure of how much to reveal about herself to the strangers at Brookfield. Lydia provocatively writes outlandish whims to her new pen pal, Seb. Seb doesn't know where the reality of Lydia ends and the fantasy begins, but automatically distrusts her because her father is a judge. Emily's pen pal Charlie takes her letter at face value, believing she is vapid and superficial - but Emily is simply seeking the approval of her English teacher with her bland letter. Cassie tells her pen pal Matthew all about her counseling sessions, but doesn't reveal why she is in therapy: her father died from leukemia the previous year, an event which deeply affected all three girls. Matthew writes back brief and violent letters, uninterested in getting to know Cassie.

As the letters continue, the pen pals slowly start to trust each other: Emily takes charge of teaching Charlie how to date, Lydia and Seb trade "covert missions" to test each other's daring, and after a great deal of one-sided correspondence, Cassie and Matthew start to bond over a mutual love of music. Lydia's "covert missions" from Seb require getting him out of his exams by pulling pranks at Brookfield. One of the pranks inadvertently involves Charlie, who believes he is saving the school from a gas leak...only to be humiliated in finding out that Brookfield doesn't use gas. As a result, Charlie obsesses about the girl who made the prank call that led to his humiliation, which happens to be Emily, on a secret assignment from Lydia. But Emily won't reveal the truth, admonishing him to let it go. All three sets of pen pals decide to meet: Emily and Charlie will go on a practice date so he can eventually win the girl of his dreams, Christina, and as time passes, Emily and Charlie begin to develop true feelings for each other. Lydia challenges Seb to a covert mission in which one of them has to recognize the other first in a public place, based not on pictures or descriptions, but their letters: Lydia doesn't know that Seb has already looked her up online, and is suspicious when he easily identifies her. Cassie and Matthew agree to meet so she can give him some information on children's rights that will help him get out of some trouble at school, but he never shows up. Lydia and Emily learn that there is no one named Matthew at Brookfield and begin to worry that Cassie is going insane. When Cassie finally meets up with "Matthew," a boy whose real name is Paul Wilson, and is cruelly taunted and mocked, the girls decide to seek revenge: steal Paul Wilson's girlfriend, Christina, away from him. It's a win-win situation: Charlie gets to be with the girl he loves and Paul loses what he loves most in the world. The plan backfires when Emily admits she really likes Charlie but before they can go on a real date, Charlie realizes Emily made the prank call to Brookfield that embarrassed him so much. Though she apologizes, he can't forgive her. Similarly, Lydia can't forgive Seb when she discovers he had seen her picture in a magazine article about her celebrity mother before they met and lied about it. Cassie, who admits she wrote to Matthew because he initially scared her, is afraid she will go through life scared like her father. Her fear compounds itself with fears that she will never follow her dream of being a singer, nor do anything to make her father proud.

Seb's anger flares after Paul maliciously recounts what he did to Cassie and he beats him up, sending Paul to the principal to get Seb expelled. Before he can get there, the girls intervene so Seb can get to an art competition he has entered. They use Paul's ego against him, tricking him into believing he has a role in a movie that films immediately. The girls think they have won their revenge, but find themselves in trouble when an anonymous witness claims they have been vandalizing Brookfield in a dangerous escalating rivalry between the schools. The teachers at Ashbury want to read Lydia, Emily, and Cassie's private papers in order to prove their involvement in the pranks, but the girls demand their right to privacy, and their lawyer parents back them up. An informal hearing is held at the school in which Emily presents a case to defend the girls' rights. Despite her fears about her own intelligence, Emily creates a solid argument in favor of teenagers' right to privacy, and wins the case. However, the girls are still the alleged vandals and stand at risk for expulsion. Seb, suspicious that the witness is Paul taking his own revenge, takes Cassie and Charlie to break into Paul's house, where they find evidence that he committed the crimes against Brookfield himself. They show up at the school meeting just in time to keep the girls from getting in trouble. Despite his sterling reputation, Paul cannot defend himself and the girls are exonerated.

As a show of unity between the schools, all the pen pals must participate together in the spring concert. The book ends happily with Emily and Charlie starting to date, as well as Lydia and Seb, who helps Lydia's dream of becoming an author come true by illustrating a book she writes. Cassie, coming to terms with how the death of her father has changed her, gets up the courage to sing a song in the concert, using one of "Matthew's" letters for the lyrics.