Lily is the tritagonist of Thomas and the Magic Railroad and the granddaughter of Burnett Stone. She lives in the city with her mother. With the help of her grandpa, Patch, and Thomas, they helped restore Lady to her former glory and returned the magic to the Magic Railroad.
- Mara Wilson
- Houko Kuwashima (Japan; voiceover)
- Gaby Ugarte (Latin America; voiceover)
- Leyla Rangel (Latin America; TV Version; voiceover)
- Marie-Luise Schramm (Germany; voiceover)
- Geneviève Déry (French speaking Canada; voiceover)
- Anat Erlich (Israel; voiceover)
- Lily has a stuffed bluebird that she takes everywhere with her.
- It's unknown if her last name is Stone or not.
- Both her Wooden Railway and Wind-up toys have her in a green shirt, depicting the outfit she wore when getting on the Rainbow Sun.
- In the original script:
- Lily, married to Patch and telling the story to her children twenty years later, was the narrator.
- Her father was away at work.
- Lily has an unborn sibling, which is the reason for her going to visit her grandfather.