Yep was born in San Francisco, California to Yep Gim Lew (Thomas) and Franche. His older brother, Thomas, named him after studying a particular saint that had died from a gruesome death (Yep, 1991). Growing up outside of Chinatown, Yep and his family lived above their family owned grocery store, La Conquista, in a multicultural neighborhood that consisted of mostly African Americans. Growing up, he often felt torn between both American and Chinese culture, and expressed this in many of his books. A great deal of his work involves characters feeling alienated or not fitting into their surroundings and environment, something Yep has struggled with since childhood. Most of his life, he has had the feeling of being out of place, whether because he is the non athlete in his athletic family or because he is Chinese and once lived in Chinatown but does not speak the language. As it says in his autobiography, "I was too American to fit into Chinatown, and too Chinese to fit in anywhere else." As a boy, Yep attended a bilingual school in Chinatown. Just like Casey Young, a character in Child of the Owl, Yep was placed in the lower level Chinese class where he was able to pass without learning how to speak the language. He later entered a Catholic high school in San Francisco where he continued his interest in chemistry and became equally intrigued with writing. His first writing was done in high school, for a science fiction magazine. His teacher, a priest, told him and a couple of his friends that to get an A, they had to get a piece of writing accepted by a magazine, and that's when he started to realize that a career in writing was meant to be.

Yep attended Marquette University and graduated from the University of California, Santa Cruz. He earned a Ph.D in English at the State University of New York at Buffalo.

While working in his family’s store, he “learned early on how to observe and listen to people, how to relate to others. It was good training for a writer” . However, as a child, he thought of himself as a scientist and he “was going to be a chemist. Like my father, I was fascinated by machines” . His decision to become a writer did not come until the time he entered college at Marquette.

During his time at Marquette University, he met and became friends with the literary magazine editor, Joanne Ryder. She introduced him to children’s literature and later asked him to write a book for children while she was working at Harper & Row. The result was his first science fiction novel, Sweetwater. According to Yep, his relationship with Joanne began as friends and progressed into love (Yep, 1991). Yep and Ryder are married and live in Pacific Grove, California.

Yep's most notable work is his series, the Golden Mountain Chronicles, which documents the story of the fictional Young family from 1849, in China, to 1995, in America. He received the Newbery Honor for two books in the series, Dragon's Gate and Dragonwings, the latter of which has been adapted into a play. Other notable books are the Dragon series and The Chinatown Mysteries. In addition, Child of the Owl won the Boston Globe-Horn Book Award in 1977 and The Rainbow People, Yep’s collection of short stories based on Chinese folktales and legends, received the same award in 1989. He was awarded the Laura Ingalls Wilder Medal in 2005 for his contributions to children's literature.

One of Yep’s central topics is individuals who feel alone and as if they do not belong in their surroundings--a feeling common to young readers. Many of his characters, through their journeys, are able to find who they are and where they belong.

A live-action/CGI TV movie of The Tiger’s Apprentice, adapted by Finding Neverland writer David Magee, is currently being developed by Cartoon Network.

Golden Mountain Chronicles, in chronological order (parentheses indicate the year in which the story is set)

1. The Serpent's Children (1849)
2. Mountain Light (1855)
3. Dragon's Gate (1867) (Newbery Honor)
4. The Traitor (1885)
5. Dragonwings (1903) (Newbery Honor)
6. Dragon Road (1939) (originally titled The Red Warrior)
7. Child of the Owl (1960)
8. Sea Glass (1970)
9. Thief of Hearts (1995)

Dragon

1. Dragon of the Lost Sea
2. Dragon Steel
3. Dragon Cauldron
4. Dragon War

Chinatown Mysteries

1. The Case of the Goblin Pearls
2. The Case of the Lion Dance
3. The Case of the Firecrackers

City Trilogy

1. City of Fire
2. City of Ice

The Tiger's Apprentice

1. The Tiger's Apprentice: Book One
2. Tiger's Blood: Book Two
3. Tiger Magic: Book Three

Ribbons (untitled group of books)

1. Ribbons
2. The Cook's Family
3. The Amah
4. Angelfish

Later, Gator (untitled group of books)

1. Later, Gator
2. Cockroach Cooties
3. Skunk Scout

Nonfiction

1. American Dragons: Twenty-five Asian American Voices (editor)
2. The Lost Garden (autobiography, part of the In my own Words series)

Picture Books

1. The Magic Paintbrush
2. The Dragon Prince: A Chinese Beauty and the Beast Tale
3. The Butterfly Boy
4. The Shell Woman and the King: a Chinese folktale
5. The Khan's Daughter: a Mongolian folktale
6. When the Circus Came to Town
7. The Ghost Fox
8. The Boy Who Swallowed Snakes
9. The Man who Tricked a Ghost

Other books

1. Tongues of Jade
2. The Rainbow People
3. Sweetwater
4. The Star Fisher
5. Dream Soul (sequel to The Star Fisher)
6. Hiroshima: A Novella
7. The Earth Dragon Awakes: the San Francisco Earthquake of 1906
8. Lady of Ch'iao Kuo: Warrior of the South (part of The Royal Diaries series)
9. The Journal of Wong Ming-Chung: A Chinese Miner (part of the I Am America series)
10. Spring Pearl: The Last Flower (part of the Girls of Many Lands series)
11. The Imp that Ate My Homework
12. Kind Hearts and Gentle Monsters
13. The Mark Twain Murders
14. The Tom Sawyer Fires
15. Shadow Lord (a Star Trek novel)
16. Mia
17. Bravo, Mia!

Plays

1. The Age of Wonders
2. Dragonwings
3. Pay the Chinaman (one-act)
4. Fairy Bones (one-act)
5. HI