Eight-year-old Doremi Harukaze aspires to be a user of magic, as she believes it would solve all her problems and help her confess to a boy she liked. One afternoon, she comes upon a magic shop and correctly suspects that the shop owner is a witch. The shop owner becomes a Witch Frog, "greenling", as this happens to witches when their true identities are discovered. In order to retain her original form, the shop owner, Majo Rika, takes Doremi as her apprentice to turn her into a witch. Doremi must take nine witch exams at night to become an official witch; however, she must never let her own identity as a witch be found out or the same fate that befell Majo Rika will happen to her.
Hazuki and Aiko find out Doremi's secret of being a witch apprentice after the stunt she pulls on Parents' Day, so they must also become witch apprentices to protect Doremi. The three girls redecorate the magic shop with a more cheerful design after Doremi accidentally destroys the shop.
Nobuko Yokokawa is a liar in the girls' class, but nevertheless amuses everyone with her imaginative stories. When Aiko believes in her and realizes she lied, she becomes very hurt.
The three girls prepare to take their first witch exam, but Doremi must spend the day supervising her younger sister Pop. Pop wants to go to her grandparent's house by train by herself. When it comes to exam time, Hazuki and Aiko earn fairies for passing the exam. Doremi fails the exam, so she doesn't get a fairy.
After failing to pass the level 9 exam, Doremi is given another chance. Her goal is to find medicine for Motamota. Luckily, Doremi passes and gets her fairy, but she does it with the help of Aiko and Hazuki, who come to see her out of worry.
Doremi's fairy Dodo runs off after being scolded, so the girls use their new magic spell, Magical Stage, to try and find her.
Miss Seki and the vice principal drop by the magic shop after photos of the girls working there arise.
After being insulted by Takao Kimura, Marina Koizumi refuses to take care of the school's flowers. Hazuki is determined to help Marina realize Kimura is remorseful.
A young boy named Misaki Shibayama trades in his favorite shirt to get a charm to help his older brother Daichi play in a soccer game.
The girls take the Level 8 Exam in which they have three hours to clear three obstacles unknowingly chosen beforehand.
Naomi Okuyama is insulted by the SOS Trio for showing her feminine side and refuses to forgive them until they make her laugh.
Majorika gets purchased by Pop. Pop treats Majorika like a plush toy and she takes her to school one day.
Doremi's father takes her and her friends on a fishing trip with a young boy who shares his passion.
Masaru Yada gets arrested, and no one else besides Hazuki and Miss Seki believes that he did nothing wrong. With Miss Seki's job on the line, Doremi, Hazuki and Aiko use their magic to find out if the rumors behind Yada are true.
After a fluke grants them immediate success on the Level 7 Exam, the girls find out that Nanako Okada refuses to take care of the school's rabbits and use their new powers to find out why. They learn that Nanako once lost her puppy and is afraid to have another pet because she thinks the same thing might happen.
On the last day without magic for breaking the laws of the Witch World, Hazuki is kidnapped by two conmen and only Doremi and Aiko can rescue her.
After noticing that the people around them are becoming ill due to Majoruka's charms, Aiko, Doremi, and Hazuki use their magic to break the spell.
With the shop under enemy control, the girls must find a way to get in to take their Level 6 Exam.
After her father gives Aiko a new harmonica and decides to throw away the old, cherished one, she runs off to Hazuki's house. There, they find an extra magic bead, which they use to gain entrance to their exam.
The girls get a hold of Majoruka's crystal ball and are challenged to a magical duel for control of the shop.
Pop is appointed as a witch apprentice after witnessing her sister and friends perform magic. She uses magic to create ghosts at her kindergarten sleepover, and Doremi, Hazuki, and Aiko help clean up her mess.
The girls receive the Purelein Personal Computer from the Queen to capture the Bad Cards that exist in the Human World. Upon start-up, they are introduced to Oyajīde, the captive wizard who let loose the cards.
Doremi comes across a cute tennis player named Yutaka Kashiwag at Hazuki's summer house and falls head over heels for him, but her snobby classmate Reika Tamaki also has an eye on him.
Doremi, Hazuki, Aiko, and their classmates head to Nobuaki Yamauchi's temple to share ghost stories and test their courage.
Upon returning to school from summer vacation, the girls become interested in their classmate Shino Hanada's trip to Mongolia. At the same time, they are due to take the Level 5 Exam.
Masaharu Miyamoto, with the support of Doremi and her friends, challenges Tamaki's bid for class president.