Note: This page is a work in progress. The production order for episodes and alternative titles are listed in notes and on their specific pages.
- Bunny Love (pilot): The Warden's plan to give all the inmates bunny costumes is quickly sabotaged by the Twins, creating a war between the population.
- Superbar: The Warden decides to build a bar in Superjail, in hope of getting to win Alice's love.
- Combaticus: After the staff discover an ancient fighting arena, the Warden decides to hold a bloody competition to get the inmates motivated.
- Ladies' Night: A carrier ship from the all-female Ultraprison becomes stranded at the jail, leading to a risky bet between the rivaling Warden and Mistress. note
- Cold-Blooded: A deadly new inmate arrives at the jail, leading the Warden to send Jared undercover. note
- Don't Be A Negaton: The motivational speaker D.L. Diamond becomes a celebrity within the jail, but Jared is willing to expose the truth behind his cult.
- Terrorarium: The Warden subjects inmates to a deadly adventure inside his Terrorarium.
- Mr.Grumpy-Pants: Jailbot accidentally brings a little girl to the jail, who the inmates quickly take an interest in.
- Dream Machine: After a nightmare convinces him that he'll be betrayed, the Warden decides to spy on everyone else's dreams.note
- Time-Police (part 1): The Warden is put on trial for crimes that he'll apparently commit in the future.
- Time-Police (part 2): The rest of the Superjail staff try to make it in the real world, while the Warden tries to find a way to escape his imprisonment.
Note: The season 1 DVD and reruns on Adult Swim arrange the episodes in their original production order, rather than the intended airing order set by the crew. The later two seasons do not have this confusion on their DVD releases.
In addition, it's also worth noting that this season would credit the writers differently. While the outlines for episodes and gags were thought up by Karacas, Warbrick, and a few other writers, the revisions and most of the actual scriptwriting duty went to people such as John Lee, Jon Glaser, and Chris McCulloch. The later seasons formally utilized a story editor and revised the writing process somewhat.
- Best Friends Forever: Jailbot and Jacknife are shot down over a mysterious island, leaving the Warden to attempt to take over Jailbot's work. note
- Mayhem Donor: The Warden decides to run a black market of dismembered body parts, after Jared winds up grotesquely mutilated.
- Lord Stingray Crash Party: A castaway finds himself at Superjail and befriends the Warden, who's oblivious to his actual intent. note
- Hot Chick: A mysterious and deadly woman arrives at the jail, and has her eye set on the Twins.
- Gay Wedding: Jean and Paul finally decide to get married, but the Warden's ideas complicate their wedding and relationship.
- Ghosts: The jail winds up infested with millions of restless undead.
- Jailbot 2.0: After Jailbot falls into disrepair, Jared brings an improved model to the jail to try to solve the problem.
- The Budding of the Warbuxx: The Warden assumes the inmate population is drugged after they refuse to enjoy his movie night. Meanwhile, Alice tries to help the Twins with an unexpected problem. note
- Superjail! Grand Prix: The annual Grand Prix is held, with the promise of freedom for whoever wins the race. note
- Vacation: The Superjail staff and inmates embark on a vacation cruise that quickly turns deadly and out of control.note
Note: While the DVD lists the episodes in the correct broadcast order, Adult Swim reruns the episodes in production order, which may create some confusion with the final two episodes.
- Stingstress: Months pass after the end of "Vacation", and the Warden must try to take back Superjail from Lord Stingray and the Mistress. note
- Superfail: After the Warden is injured in an accident, Jared attempts to run the jail his way but must face off against the Doctor's escaped mutants. note
- Uh Oh, It's Magic: The Warden attempts to learn magic, but finds that his ventriloquist dummy is threatening to steal his fame. note
- Sticky Discharge: Superjail must face its first paroled inmate, much to the Warden's despair. note
- Special Needs: The Warden attempts to integrate a very special group of inmates into the general population.
- The Trouble With Triples: The Twins' guests interfere with the Warden's plan to create a virtual reality game in Superjail. note
- Nightshift: Alice winds up becoming a chef and surprises others with her talent, leading to jealousy and chaos ensuing.
- Oedipus Mess: Jacknife becomes a father but escapes, leading the Warden to create 10,000 clones to determine which will be the best parent for the new baby. note
- Planet Radio: The Warden must fight back against a pirate radio station competing with his new TV network.
- Burn Stoolie Burn: Ash and the Warden form a friendship, one that could potentially destroy everything. note
Note: Adult Swim at first confused the scheduling of air dates of several episodes, due to the scripts being written in a much different order than what went into production (as well as the episodes' intended airing order). This lead to a department accidentally airing a promo for "Uh Oh, It's Magic" as an advertisement for the season premiere, as well as having several other errors in their schedule during the early run.
The reruns of season 3 also use the script order listed in the notes, which leads to the above season finale being aired much earlier.
- Superhell!: In a continuation to "Burn Stoolie Burn", Superjail continues to burn to the ground while Alice must (inadvertently) enlist the help of Ultraprison.
- The Last Pack: A ban on tobacco causes the inmates to do anything to get their hands on a pack of cigarettes.
- Jean & Paul & Beefy & Alice: The Gay Inmates, Alice, and Beefy go on a spa trip that soon becomes plagued by a disease- courtesy of the Twins, who attempt to provide Jailbot with an opportunity to bond with the Warden.
- The Superjail Inquisitor: The Warden starts to believe in a fairy tale creature with a twisted moral code, and aims to convert the rest of the jail into believing in its power along with him.
- Superstorm!: The Warden's weather robot goes out of control and threatens to destroy Superjail with its weather powers.
- The Superjail Six: The Warden gets captured by a gang of reptilian hillbillies after Stingray and Peedee take advantage of the legend of six inmates who managed to escape Superjail.