Van Eekhout's parents are of Indo (Dutch-Indonesian) extraction. His last name (meaning "of Oakwood") is pronounced "like this: Van, as in the kind of thing you drive, eek, as in, 'Eek, killer robots are stomping the rutabagas!' and hout, like 'out' with an h in front of it. The emphasis is on the Eek."
He grew up in Los Angeles and attended UCLA, where he received a Bachelor's in English. He earned a Master's in Educational Media and Computers at Arizona State, and worked for a time at ASU designing multimedia.
He attended the writing workshop Viable Paradise in 1999. His first professionally published story, "Wolves Till the World Goes Down," (2001) appeared in the anthology Starlight 3 and was later reprinted in Fantasy: The Best of 2001. His story "In the Late December" (2003) was nominated for Nebula Award for Best Short Story. His work has also appeared in a number of other places, including Asimov's Science Fiction, Realms of Fantasy, the Magazine of Fantasy and Science Fiction, and Strange Horizons.
His first novel, Norse Code, an adult urban fantasy, was published by Bantam Books in May 2009. His second novel, a middle-grade fantasy titled Kid Vs. Squid, was released by Bloomsbury Children's USA on May 11, 2010. The Boy at the End of the World, also a middle-grade fantasy, was released in June 2011 by Bloomsbury Children's USA.
His fourth novel, California Bones, was published by Tor Books on June 10, 2014. It is the first in a planned trilogy based on his 2006 short story "The Osteomancer’s Son", anthologized in Year’s Best Fantasy 7 and Best Fantasy of the Year: 2007. The second in the series, Pacific Fire, was published on January 27, 2015.
He currently lives in San Diego, California.