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The Commander and Jetstream are two superheroes who live in a suburban lifestyle and work as real estate agents under the names Steve and Josie Stronghold, as well as help the city. Their son, Will, tries to live up to the family name, but has yet to reveal such powers.
In the airborne high school, "Sky High", Will fails the Power Placement, the test that determines whether you will be a hero or sidekick based on your abilities. He is told by the nurse that he may never receive any superpowers whatsoever even though he was born to two superhero parents. His only possibility of potentially acquiring powers is to fall into toxic waste (which is just as likely to kill him). At the end of his first day at high school, the Commander entrusts him with the 'key' to the family's Secret Sanctum (after promising that he will never bring anyone else there); the place where all the family's trophies of past victories are kept, including a strange device called the "Pacifier". The Commander tells Will about how the Pacifier was taken from an arch-enemy supervillain named Royal Pain, but little else is mentioned of Royal Pain's demise or the Pacifier's powers. Later in the evening, Layla meets Will on the roof of his house and comforts him about his situation.
Will manages to cope through his school experience, spending all his time with his fellow sidekicks, and his best friend Layla, however, they suffer bullying from the students classified as "Hero". Layla has the mysterious ability to manipulate plants; but as she refused to show it in Power Placement, she has also been ranked as a sidekick. The sidekicks are trained in Hero Support class by a retired sidekick who had once worked with the Commander, but is unknown to Will since his parents had never made mention of him. Will finally reveals to his father that he is only a sidekick and admits that he has no superpowers, but his father still maintains the belief that he will yet turn out to be a great superhero. Meanwhile, in their living room, Will's friends overhear his conversation with his father about being proud that he is a sidekick; when he returns, they look at him in silent admiration and gratitude.
Will's strength superpower eventually manifests itself during a fight with Warren Peace, whose supervillain father, Baron Battle, was defeated by the Commander. The fight is ended after the principal takes them to the special detention room, which is designed to neutralize all super powers. Will attempts reconcile with Warren, but he will have nothing to do with him and vows to retaliate at first opportunity. Meanwhile, Will is moved from Hero Support class to Hero class. In his new class, he is partnered with Gwen Grayson, a senior who is a technopath, meaning she can control technology with her mind. Will has an enormous crush on her, dating back to the day they first met, and the two develop a relationship. As he proves his powers, he begins to grow more and more distant from his friends, including Layla, and eventually ends up standing her up for a dinner appointment in favor of hanging out with Gwen. Layla meets up with Warren Peace at the restaurant, and eventually the two end up forming a sort of alliance, designed to get back at Will and make him jealous of them as a 'couple'.
Gwen meets the Strongholds and invites them to be the recipients of the very first Hero of the Year Award, which will be presented at the Sky High Homecoming Dance. She also invites Will to be her official date for the event. Gwen unexpectly uses Will's house to throw a party for the heroes while his parents are saving the city. Using the excuse of wanting to talk alone, Will breaks his promise and takes her to the Secret Sanctum. Gwen also uses the party as an opportunity to tell Layla what Will 'really' thinks of her, and Layla leaves the party in tears. Will, when he hears what Gwen has done, breaks up with her the night before the dance, forces everyone out of the house just as his parents arrive. He also tries to reconcile with Layla to no avail, and decides not to go to the dance after all. He visits the Secret Sanctum and realizes that the Pacifier has been stolen, and that Gwen is the reincarnation the person who invented it in his father's high school yearbook. Meanwhile, the Commander and Jetstream arrive at Sky High. During Gwen's presentation of the award, it is revealed that she is Royal Pain and she unveils the Pacifier. The Commander, Jetstream and many others attempt to stop her, she turns them back into infants.
The sidekicks band together in an attempt to stop Royal Pain and each has a chance to exercise their superpowers to full potential. Will arrives at the school, and meets up with his friends, who begin to tell him about Royal Pain. He reconciles completely with Layla, then takes on Royal Pain alone, and while fighting her, is thrown out the window and off Sky High. Will's flying power manifests itself and returns to defeat Royal Pain, who having been turned back into an infant when the Pacifier broke the first time, grew back up with intent to return and kidnap superheroes to raise all over again as supervillains. The defeated Royal Pain triggers the sabotaged anti-gravity device, causing Sky High to fall. Will flies out of the window and prevents the school from touching down while his friends quickly work to repair the device. The device is repaired, and the school returned into the sky. The infants are all returned to their adult state by reversal of the Pacifier's powers, and Royal Pain and her minions are given time to cool off in the detention room.
Will and Layla engage in a passionate kiss while suspended off the school grounds in mid-air.
In the end, not only Will and Layla started dating, Royal Pain and her gang are now in jail, Warren and Will are now best friends, and Ron Wilson, the bus driver for the school who was born with no powers to superhero parents, was covered in toxic waste that gave him the power to become a giant and now works for the mayor to stop giant robots.
- Michael Angarano as William Theodore "Will" Stronghold: a freshman at Sky High. His parents are the two most famous superheroes - Commander and Jetstream - of the day. It is not revealed that he has superpowers until later on in the movie. He has both super strength and flight. He and his best friend Layla become a couple at the end of the movie.
- Danielle Panabaker as Layla Williams: Will's best friend who has the power of plant manipulation; they have been best friends since childhood. She is a pacifist and a vegetarian and is able to animate and control plant life, put into the sidekick program because she refused to showcase her abilities because she doesn't believe in the system. She has a crush on Will throughout the movie, and in the end the pair share a kiss, floating outside the school.
- Mary Elizabeth Winstead as Gwen Grayson/Royal Pain: a senior at Sky High; Will has a crush on her. She is the main antagonist of the film. Her power is technopathy. She was jaded at being placed as a sidekick the first time she grew up due to the then obscureness of her powers. Winstead said of her role, "I bounced around. I was either the hero of the sidekicks or the sidekick to the heroes."
- Steven Strait as Warren Peace (a play on the novel War and Peace): the son of an unnamed superheroine and a supervillain known as Baron Battle (who is mentioned to be in jail with several life sentences). He is pyrokinetic, meaning he can control and manipulate fire. He comes best friends with Will at the end of the movie.
- Dee Jay Daniels as Ethan: A Hero Support who is friends with Will, he can instantanously shift between human and a small orange puddle (which earned him the nickname "Popsicle").
- Kelly Vitz as Magenta/Maj: Will's friend whose ability is to shapeshift but only into a guinea pig complete with purple highlights/streaks in her fur.
- Nicholas Braun as Zach Braun/Zack Attack: Will's spacey friend, who has the ability to glow in the dark, he maintains the belief that he is hero material and that his power is amazing. He always wears white/fluorescent colours. He is also shown to like Magenta.
- Malika Haqq and Khadijah Haqq as Penny: Gwen's best friend/ henchmen, who can duplicate herself and is therefore the entire cheerleading team.
- Jake Sandvig as Lash and Will Harris as Speed: the resident bullies at Sky High. Lash is skinny, and can stretch his body parts, while Speed is overweight yet can run at super speed.
- Kurt Russell as Steve Stronghold/The Commander: Will's father. As the Commander, he is one of the world's strongest superheroes, displaying superhuman strength and durability, and a successful businessman in his secret identity.
- Kelly Preston as Josie Stronghold/Jetstream: Will's mother, Josie Stronghold, a successful real estate agent. As Jetstream, she can fly and is touted as being an expert in hand-to-hand combat.
- Lynda Carter as Principal Powers: the principal of Sky High. She appears to have the power to transform into a comet and back at will. She mainly uses her power as a form of transportation.
- Bruce Campbell as Coach Boomer/Sonic Boom: the gym teacher at Sky High, also known as Sonic Boom due to his ability to release sonic waves from his vocal cords, which he conveniently uses to bark at any student who doesn't live up to his expectations. His power is known as sonic screaming.
- Kevin Heffernan as Ron Wilson - Bus Driver: the Sky High bus driver/pilot. Ron is the son of two superheroes but does not have any powers himself. He feels a great sense of pride in driving the "superheroes of tomorrow" to school.
- Cloris Leachman as Nurse Spex: a kind and eccentric elderly lady that serves as Sky High's single known nurse, with the ability of X-ray vision.
- Jim Rash as Mr. Grayson/Stitches: Royal Pain's bumbling sidekick.
- Dave Foley as All American Boy/Mr. Boy: The Commander and Jetstream's old Hero Support. He now works as Hero Support teacher at Sky High. Though he tries to appear chipper and tries to inspire his students he is quite clearly unhappy and living in past glory. His first name is Jonathan.
- Kevin McDonald as Professor Medulla: the Mad Science teacher, with super brainpower – so much that even as a baby he is still more intelligent than the average adult.
- Kim Rhodes as Elastically/Professor Elast : she is a very competitive and kind, she has a crush on Coach Boomer, she is only shown in the deleted scenes of the movie. Her first name is Jeannie.
- Tom Kenny as Mr. Timmerman makes a small cameo in the movie. He is best known as the voice of SpongeBob SquarePants.