The movie has its world premiere at the Berlin film festival on Friday, and is the last of 18 competition entries to screen. The annual cinema event, also known as the Berlinale, closes with an awards ceremony on Saturday.
Nguyen, who has been thinking about and working on the project for 10 years, said he had been told by a friend to film only what he knew.
"Through the course of writing this script, I don't know why, but I could relate tremendously with this girl," he told reporters after a screening where the film was warmly applauded.
"It's more about trying to talk about what you can feel rather than what you know."
War Witch was filmed in Democratic Republic of Congo and used a mixture of trained actors from Canada and Congolese newcomers, including the young female star Rachel Mwanza.
She plays Komona, a 12-year-old girl whose peaceful life in a village is shattered when rebels arrive, kill most of her neighbors, force her to shoot her own parents and leave with a dozen or so child recruits.
After surviving a jungle skirmish with government forces, Komona is elevated to status of "witch," meaning she is treated with respect by the rebels but is also chosen to be rebel leader Great Tiger's concubine.
All the while she is haunted by the ghosts of her parents, who beckon her to lay their souls to rest if she ever wants peace. She falls in love with an albino rebel called Magician, a relationship that brings temporary respite from her suffering.
Nguyen said he deliberately used non-conventional story-telling techniques such as the ghosts to reinforce the childish vision he wanted to create.
"I wanted to do this film as if I was a young child, a 14-year-old director who didn't know the politics.
"I wanted to try to project the film that's seen from the eyes of this character. I guess that the politics of it are filtered through a child's eyes. I didn't want this to be an education film."
There is humor amid the barbarity of killings, executions and slavery, as when Komona sends Magician on a quest to find a white rooster if he wants to marry her.
Laughed at for falling for the oldest trick in the book -- apparently there are no white roosters -- Magician nonetheless tracks one down, underlining a determination and heroism that marks him apart from the fighters around him.
Mwanza, from Kinshasa, told a press conference that she was abandoned by her parents as a child and taken in by her grandmother, who then also sent her on to the streets when she could no longer cope.
She appeared in a documentary film and gave the money she earned to her grandmother to pay for her education, but when it was used for other purposes she left for a refugee centre.
"It's a kind of miracle, if I can put it like that, that I was kept on after the first film," she said through an interpreter.
"Then I learned to read. I am very proud to be able to read now. I don't have a family any more, the people you see on each side of me are my family now."