Navarro-Canales wore a navy jail uniform and handcuffs when he entered the plea during a brief court appearance Monday in Las Vegas.
The Henderson teenager is suspected in the stabbing deaths of his 40-year-old mother, Elvira Canales-Gomez, and 9-year-old brother, Cesar Navarro.
The discovery of their bodies in their apartment on Sept. 20 touched off a six-day manhunt for the teen that extended to the U.S.-Mexico border.
He was later found sitting in a food court along the Las Vegas Strip.
Navarro-Canales was charged as an adult with two counts of murder.
A cousin and three others who attended the court hearing didn't comment to reporters afterward.