Matilda is first seen as a newborn baby in a hospital. Later, she is taken by her nasty parents and put in the trunk of the family car rather than being held by her mother or being buckled in. She ignores Michael when he tries to play with her. When she gets older, she makes a mess with boiled spinach and writes her name in it with her finger, only to disgust her mother.
By the time she is two, Matilda learns how to take care of herself by cleaning up her face, getting down from the countertop safely, buckling her shoes, getting dressed, and even tying her own hair ribbon. She was always left home alone, but she liked it. In fact, she learned from reading how to cook. She read every book in the house by the time she was four. Then she asked her father for a book, much to his dismay. So, she had to get a book herself and find the children's library, where she walks by herself every time Michael is in school, Harry is out selling used cars, and Zinnia is out playing bingo.
Finally, when she is six, her parents cannot bear her reading any longer, and they dislike her idea of her going to school, which she wants to do. Later, for having explained the amount of money Harry sold a car for, she is accused of cheating and is sent to her room for "being a smart-alek". She attempts to punish her angry parents by having him accidentally bleach his hair and by adding "super-super glue" to the inner brim of his hat. At home, while she is reading Moby Dick (from the library), and her father gets very furious for this instead of eating any dinner and watching TV and rips the book. As he is forcing her to look at the TV, she passively destroys it with powers she didn't know she had.
Another time, Matilda is sent to Crunchem Hall School, where she meets a girl named Lavender and an older one named Hortensia, the latter of which explains about an iron-maiden-like device called the "chokey". She also ends up meeting the cruel principal, Miss Agatha Trunchbull, who swings a pig-tailed girl named Amanda Thripp and throws her around the fence. She then meets her nicer teacher Miss Honey. After school, she tries to explain her day at school to her mother, but she doesn't care. That night, Miss Honey comes to talk to Mr. and Mrs. Wormwood about Matilda, who is then sent to her room. After a talk, Miss Honey gives a book to Matilda.
The next day, Matilda is called in with the other kids to the assembly room immediately to watch an obese boy named Bruce Bogtrotter being forced to eat a whole chocolate cake. Matilda starts encouraging Bruce to keep going until Miss Trunchbull breaks the plate over Bruce's head and he burps. Along with the other kids, Matilda is forced to spend five hours after school staying and copying from the dictionary, with a threat that anyone who objects will go right into the chokey together. It isn't until nighttime that Matilda goes home, and her father accuses her of lying when she explains what happened, because she wasn't there to take any packages out on the doorstep in. Throughout the story, Matilda learns that Miss Honey was Miss Trunchbull's niece and the vile principal had murdered Miss Honey's father. So she and the other students, with Miss Honey, band together and, aided by Matilda's mind powers, defeat Miss Trunchbull, driving her out of Crunchem Hall forever. At the end, Matilda wants to stay with Miss Honey since her family is moving to Guam. Harry and Zinnia reluctantly agree to sign the adoption papers and let Matilda stay with Miss Honey for the rest of her life.