[1][6] Lee's debut young adult science fiction novel, Zeroboxer, was published by Flux Books and nominated for the 2016 Andre Norton Award.

[19] Her debut novel for adults, Jade City, the first in The Green Bone Saga, was published by Orbit Books in 2017 to critical acclaim.

[5][35] In 2022, Subterranean Press published Lee's standalone novella set prior to the events of The Green Bone Saga entitled The Jade Setter of Janloon.

[36] In 2020, it was announced that a TV series based on Jade City was being developed at Peacock, with Lee serving as a consulting producer.

[42] In March 2023, Orbit Books announced that it had acquired the rights to Fonda Lee's "cyberpunk samurai space opera" novel The Last Contract of Isako, which is scheduled for winter 2025.