- Sweet Clara and the Freedom Quilt (1993)
- Maria's Comet (1999)
- Pioneer Summer (2002)
- Girl Wonder: A Baseball Story in Nine Innings (2003)
- Shutting Out the Sky (2003)
- Apples to Oregon (2004)
- Sky Boys (2005)
- Into the Firestorm (2006)
- Abe Lincoln Crosses a Creek (2008)
- Keep On! The Story of Matthew Henson, Co-Discoverer of the North Pole (2009)
- Titanic: Voices from the Disaster (2012)
- The Great Trouble: A Mystery of London, the Blue Death, and a Boy Called Eel (2013)
- Steamboat School (2016)
- A Letter to my Teacher (2017)
- Sweet Clara and the Freedom Quilt won the International Reading Association Award.
- Sky Boys, about the builders of the Empire State Building, was a Boston Globe–Horn Book Award Honor book.
- Keep On!, about Matthew Henson, won the Eloise Jarvis McGraw Award for Children's Literature for 2009/2010.
- Titanic: Voices from the Disaster was a Robert F. Sibert Honor book and a YALSA Excellence in Nonfiction finalist.
- The Great Trouble, a novel about Dr. John Snow and a cholera outbreak in Victorian London, was an Oregon Book Award finalist and winner of the Oregon Spirit Award.
- Steamboat School, about John Berry Meachum and his students, received the 2017 Jane Addams Children's Book Award, given annually to a children's book that advances the causes of peace and social equality.
- Two of her books won a Jane Addams Book Honor Award in 2004: Girl Wonder: A Baseball Story in Nine Innings about Alta Weiss, for younger readers and Shutting Out the Sky, about immigrants in 1900s New York, for older readers.
- Shutting Out the Sky was also an NCTE Orbis Pictus Honor Book.