Emily Byrd Star is a creative and lonely girl who keeps herself company with imaginary friends such as the Wind Woman and Emily-in-the-Glass. She lost her mother as a baby. When her father dies of consumption, Emily finds that her largely unknown, extended family members discuss who must care for her. Though most don’t want the responsibility, they pick slips out of a hat — and the Murrays of New Moon are chosen.
Elizabeth and Laura Murray are spinsters. They run a farm with their cousin, Jimmy. Jimmy is said to be a little odd in the head, supposedly because in his youth, the strict and strong-willed Elizabeth pushed him down a well. Out of all of their relatives, Emily is drawn to Elizabeth’s sister, Laura. Laura’s gentle ways and kind soul immediately make Emily feel a bit more at home.
While at first she doesn’t know if she will enjoy living on the farm, Emily soon falls in love with the green fields and quiet nooks of New Moon. Emily is a spirited writer and finds solace in writing letters to her father every night as a way to work through the day’s events and still remain connected with him. Emily soon finds a kindred spirit in cousin Jimmy’s soft-spoken ways and the rustic poems he pens.
Emily discovers many romantic vistas and stories surrounding New Moon — such as the Disappointed House she passes on her way to school. Though nearly finished, the house was abandoned when a woman jilted the man building it.
When Emily starts school, she realizes she likes learning and its community of young people — a contrast to her father’s home-schooling. Although she has some trouble with making friends and is initially bullied by a girl named Rhoda Stuart, she meets a wild, blond beauty who comes to her rescue. Ilse Burnley is the daughter of the town’s doctor, a man who is known for his notorious refusal to believe in God. His wife left him when Ilse was a baby, breaking his heart and shattering his faith.
Emily and Ilse officially become friends when Emily wanders in the woods surrounding New Moon and stumbles upon Ilse. A thunderstorm blows in, and the girls hole up in Ilse’s house to escape the downpour. They spend the night chatting and trading stories.
The girls attend school together, play games and have fights. Many of the fights include Ilse blowing up about something and firing off a colorful array of insults, while Emily calmly smiles and interjects the occasional witty comment. Eventually, Ilse cools down and carries on as if nothing happened. Once Emily finds a way to manage Ilse’s tantrums, she soon finds that beneath her spitfire ways, the girl is loyal.
One day, some time into their friendship, the girls are told by Ilse’s father to wander up to the Tansy Patch, where a boy named Teddy Kent is getting over an illness and could use some fun and sunlight. Although Teddy’s mother is rather odd and unfriendly, Emily decides immediately that she likes Teddy. His quiet charm and artist’s eye are like dashes of color and whimsy that resonate with her.
Before long, Teddy has joined Emily and Ilse’s close-friend group, and they spend October hanging around cousin Jimmy, as he boils the pig’s potatoes. Jimmy recites poetry, Teddy lies on the ground sketching the scenes stretching out around them and Emily and Ilse dance in the grass. It’s a wonderful time and even Ilse admits that at moments like this, she believes there could be a God.
A few weeks later, Emily makes another friend, Perry Miller. While walking home across a field, Emily is chased by a bull. Before it can catch her, a lanky boy leaps over the fence and draws the bull’s attention away so Emily can escape. He escapes the bull by climbing back over the fence.
Perry is outgoing and good-natured. New Moon takes Perry on as a hired hand when they find he is in need of work. They also decide it is time to send him to school with Emily, as Perry is determined to better himself and is a quick learner.
Perry and Teddy don’t get along quite as well as Emily would like, which is due to a crush the boys both have on her. And Ilse doesn’t seem to like Perry much either. His incessant teasing of Teddy makes her angry, as she has a crush on Teddy.
The next year of Emily’s time at New Moon is filled with one adventure after another — from a scare with a supposedly poisoned apple to a night spent with Ilse in which their house was nearly lit on fire. When Teddy draws a picture of Emily smiling, with her hair styled so that she has bangs, the girl decides that she truly does want to have bangs. She accidently cuts them ridiculously short, and they look uncomely.
Despite the horrible haircut, when Emily’s great-aunt Nancy asks to see a picture of Emily, Elizabeth tells Emily it has to be one featuring the tiny bang, if pinned back. Ashamed of her own appearance, Emily instead sends the Smiling Girl sketch that Teddy created.
Emily is even more shocked when Nancy replies, saying that she liked the sketch of Emily very much and wants the girl to visit. Although Emily is sad at the thought of leaving her friends to visit her great-aunt, her curiosity gets the best of her.
Emily journeys to visit Nancy, and although Nancy and her cousin Caroline are very opinionated and abstract, they are kind to Emily, and she has a good time with them.
One night she goes for a long walk through the woods and sees a beautiful little aster tree. But as she reaches for it, she suddenly realizes she’s come to the edge of a ledge. It gives way beneath her, dropping her to an even more precarious ledge below it. Emily lays spread eagle, tears in her eyes, painfully aware that if she moves a muscle the ledge could give way and she would fall to the boulders beneath.
Knowing that no one will be looking for her, she begins to pray desperately for help. She’s afraid if she screams she’ll rock the ledge.
Just when she’s beginning to think she may die, she hears the footsteps of someone passing by. Dean Priest, one of Nancy’s younger relatives, and the man with a slight shift in his stature that gave him the unseemly nickname of Jarback, saves Emily.
He escorts her home, and she finds that he is also an imaginative spirit. He teasingly compares her to a pixie and tells her that she has eyes like stars. He makes a veiled mention that although Emily is younger than him, with her old soul and starlit eyes, she may someday be something more than just a friend. She spends the end of her time at Nancy’s in Dean’s whimsical company, and then he drives her back to New Moon.
A few weeks back at New Moon, Emily suddenly becomes sick. She is feverish, sometimes unconscious — so much so that everyone is worried she may not pull through. In her sickness, she begins to hallucinate and screams out, “She didn’t do it!” over and over again.
Then, in a moment of clarity, she wakes long enough to ask Elizabeth to search the old well. Not wanting to make Emily’s condition worse by ignoring her strange claims, Elizabeth and Jimmy go and uncover the old well close to the Burnleys’ land. There they find the remains of Ilse’s mother.
Emily’s fever breaks, and she explains that while sick she saw a kind of vision of Ilse’s mother falling down the well. The Murrays are shocked, but admit that some of their ancestors were said to have some kind of second sight.
Whatever way Emily was able to solve the mystery of Ilse’s mother’s disappearance, the Burnleys are eternally grateful. Knowing that his wife didn’t abandon him allows Dr. Burnley to finally move on from her death — and restores his faith in God. It also gives him a new love for Ilse.
Emily quickly regains her strength, but even when she returns to school and her time with her friends, she has changed. A part of her soul has grown past childhood, and she is now entering womanhood. She stops writing letters to her father and her poems, and works to become a published author.