Waititi started developing Boy soon after finishing Two Cars, One Night and it first emerged as a film called Choice. It was accepted into the Sundance Writer's Lab in 2005 where Waititi workshopped it with script writers Frank Pierson, Susan Shilliday, David Benioff and Naomi Foner Gyllenhaal. Instead of making Boy his first film Waititi went on to make Eagle vs Shark and continued to develop the screenplay over the next three years. When the script was finally ready there was a small window of opportunity in which to make it.

Waititi dropped the title Choice because he felt that it would not translate to international audiences, and the film was retitled The Volcano. "It was a big pain about this kid’s potential to be bigger than he is or just bloom or explode... So it was a character in the script as well. When we were shooting the film it was still called Volcano and during the editing. We ended up cutting a lot of the stuff out," he says.

Waititi wanted to shoot the film where he grew up in Waihau Bay. It was a summer film but impossible to shoot in the height of summer due to the popularity of the area as a fishing and holiday destination. The film features the maize fields and the maize is harvested from late April. Boy was shot entirely in the area of Waihau Bay, New Zealand. James Rolleston was never actually intended to play the lead role of "Boy". Rolleston originally turned up on set for a costume fitting as an extra and after short deliberation the teen was offered the role.