- Newbery Honor Award for "Judy Moody and the Not Bummer Summer" (2011)
- Theodor Seuss Geisel Honor Award for "Stink and the Ultimate Showdown" (2009)
- California Young Reader Medal for "Judy Moody and the Not Bummer Summer" (2012)
- Rhode Island Children's Book Award for "Judy Moody and the Not Bummer Summer" (2012)
- Georgia Children's Book Award for "Judy Moody and the Not Bummer Summer" (2013)
- Iowa Children's Choice Award for "Judy Moody and the Not Bummer Summer" (2013)
- Keystone State Reading Association Children's Book Award for "Judy Moody and the Not Bummer Summer" (2013)
In addition to these, Megan McDonald has also been recognized by the American Library Association, the Society of Children's Book Writers and Illustrators, and the National Education Association for her contributions to children's literature.