Jim McAllister (Matthew Broderick) is a much-admired high school history teacher living in the suburbs of Omaha, Nebraska, who is actively involved in many after-school activities, one of which is overseeing the student government election process.
Tracy Flick (Reese Witherspoon) is an overachieving junior with an insufferable air of self-importance. She lives with her bitter and divorced mother who encourages her to "to whatever it takes" to succeed in life. Earlier in the year, another teacher, Jim's best friend Dave Novotny (Mark Harelik) was fired from his job and divorced by his wife, Linda (Delaney Driscoll) after it came out that he and Tracy were having a sexual affair, while Tracy's reputation was unscathed.
Against this backdrop, Tracy announces that she is running for student council president. Initially she is unopposed, as she is widely seen as the natural candidate for the job. When Tracy presents Mr. McAllister with her list of nominating signatures to qualify for the election ballot, she makes a remark about "working closely" together... which he interprets as an indication she may later try to seduce him as she did with Dave. Perhaps annoyed by Tracy's presumptuousness, and/or concerned that he might give in to this seduction and share the same fate as his friend Dave, Mr. McAllister decides to persuade junior Paul Metzler (Chris Klein), a slow-witted, but affable and popular football player to enter the race. Paul is unable to play football as he is recovering from a ski injury that resulted in his left leg being broken, and Mr. McAllister suggests a new way to explore his talents through student council. Although Paul is ambivalent at first, he agrees to run, much to Tracy's consternation.
Meanwhile, Paul's adopted younger sister Tammy (Jessica Campbell) is rejected by her romantic interest Lisa (Frankie Ingrassia), who dismisses their time together as "experimenting." Lisa then engages in a passionate relationship with Paul. In retaliation, Tammy decides to run for school president as well. During a school assembly to hear the candidate's speeches, after Tracy only draws polite applause and Paul is barely able to read his speech, Tammy announces that the office of school president is useless and promises nothing, except to try and dissolve student government. The speech rallies the students to a standing ovation, but her subversive diatribe results in her getting a suspension from school.
While working on another project after school, Tracy has an uncharacteristic fit of rage and destroys all of Paul's campaign posters. She then drives to a local power plant to dispose of the shredded posters in a nearby dumpster. Unbeknownst to Tracy, her attempted cover-up is witnessed by Tammy who was meditating near her favorite spot, an electric substation. The next day, when Mr. McAllister confronts Tracy about the missing posters and lectures her that "all of our actions can carry serious consequences," Tracy adamantly claims innocence, despite his insistence that all evidence points to her as the chief suspect. At that moment, Tammy knocks on the door and tells Mr. MacAllister she knows who tore down the posters. Tracy is asked to wait outside the room while Tammy speaks to Mr. McAllister. Tracy experiences a moment of sheer panic when she peers in the window only to see Tammy revealing the shredded posters. What Tracy can't hear is that Tammy is falsely confessing to a skeptical Mr. McAllister that it is she, not Tracy, who perpetrated the poster sabotage. As a result, Tammy is disqualified from the election and expelled from school. Tracy is now off the hook. But this clearly does not sit well with Jim, who still suspects Tracy is the guilty party. Meanwhile, Tammy's punishment of being sent to an all-girls Catholic school secretly pleases her and is the reason she took the blame for the vandalism.
The day before the election, Linda Novotny asks Jim to come over to help unclog her bathtub drain. After Jim completes the job, Linda unexpectedly initiates a sexual liaison with him and then suggests that he book a motel room for them to continue their dalliance later that day, a proposition Jim himself had half-jokingly made to Linda shortly after her breakup with Dave. However, Linda apparently has a change of heart and is nowhere to be found when Jim arrives at her house to pick her up for their tryst. Not knowing where Linda could be, Jim walks into her backyard where he has the misfortune of being stung by a bee on his right eyelid, causing a terribly painful and unsightly allergic reaction. He then drives back to the motel and desperately tries to reach Linda by phone, but to no avail. Jim eventually returns to his own house later that evening only to find Linda and his wife (Molly Hagan) huddled together crying in the living room. Realizing that Linda has disclosed the infidelity to his wife and that he is no longer welcome at home, Jim spends a miserable night sleeping in his car outside Linda's house.
The next day election day Jim oversees the counting of the ballots, though by now his right eyelid is grotesquely swollen and almost completely shut as a result of the bee sting. Paul had voted for Tracy, feeling that it would be arrogant to vote for himself. But this turns out to be a costly decision. The ballots are meticulously counted by a duo of student auditors, who determine that Tracy has prevailed by a single vote. It is then up to Jim to perform a final ballot count to certify the outcome. When Jim happens to spot Tracy dancing excitedly in the hall, he deduces that she may have been tipped off about the vote count. Angered by Tracy's unseemly display of glee and her dirty-tricks campaign tactics, Jim decides to take matters into his own hands by surreptitiously disposing of two of Tracy's ballots and declaring Paul the official victor. This turnabout elicits incredulity and shock from the two student auditors, who are certain that their original vote count was accurate. Tracy is shocked and despondent upon hearing the unexpected news of her defeat. Jim goes to the same motel he intended to commit adultery in, only this time to actually use it for lodging.
The next morning, Jim wakes up and is confident of patching things up with his wife now that the election is behind him. However, the school janitor, to whom Jim had been unknowingly rude earlier by creating unneeded extra work for him, discovers the two discarded ballots in the trash and presents them to the principal. When Jim is confronted with the evidence of his fraudulent intervention, he admits everything and resigns from his job. The rigged election becomes a nationwide email trope, and as a result Jim's wife fails to forgive him.
Divorced, publicly humiliated and ostracized by everyone he knows for this one half-hearted attempt to thwart Tracy's evil schemes to win the election, Jim leaves Nebraska forever, choosing to fulfill his longtime dream of moving to New York City, where he becomes a tour guide at the American Museum of Natural History and begins a quiet relationship with a new woman.
After serving her senior year as the new hard-line and strict dictator-like class president, Tracy graduates at the top of her class and gets accepted into Georgetown University in Washington D.C., with a full scholarship and a desire to go into politics as both her major and future career, but she soon finds the experience disappointing. Despite having gotten everything she ever wanted in life, Tracy still has no friends, no social life, and cannot fit in anywhere at the university as most outgoing students there have slid-on-by connections. Tracy comes to accept the fact that it is indeed lonely being at the top of everything.
Despite losing the student body president election, Paul enjoys a mostly happy-go-lucky senior year highlighted by being elected homecoming king and prom king, though he ends up getting dumped by his girlfriend, Lisa. After graduation, Paul gets into the University of Nebraska with a scholarship of his own where he joins a popular fraternity, makes many new friends, and resumes his career at playing football for the university.
The misanthropic Tammy becomes romantically involved with a fellow student at the all-girls Catholic school that her parents made her enroll, and later runs away with her for places unknown.
Jim's friend, Dave, moves to Milwaukee, Wisconsin and takes a low-paying job stocking shelves at a local supermarket.
As the film draws to a close, the film skips forward seven years after Jim's dismissal from Nebraska where Jim recalls a final encounter he had with Tracy. On one cold winter day, Jim is at a conference in Washington D.C. and while walking the streets, he sees Tracy from a distance as she enters a limousine outside a fancy hotel with a congressman (revealed to be Mike Geiger, a Republican representative from Nebraska) whom she appears to work for as a member of his congressional staff. Suddenly enraged at the thought of Tracy, yet again, lying, cheating, seducing and manipulating her way into political success for her own selfish reasons, Jim hurls a soda cup at the limousine, and then makes a quick getaway.
The film ends with Jim safely back in New York City at his tour guide job posing questions to a group of young elementary school children who are visiting the museum, deliberately ignoring the raised hand of an overeager little blonde-haired girl who reminds him of the ruthless and insufferable overachiever Tracy Flick.