Disclosure: I received complimentary products to facilitate this post. All opinions are my own.
Chad Cramer recently published Lights Out: Helping Your Kids Overcome Their Fear of the Dark. This book provides great ways to help your children get over the hurdle of nighttime fears, while framing everything from a Christian perspective.
It's actually similar to what we did with our oldest daughter. When she had fears of the dark (or anything else), we would follow the "what if?" trail until she realized that God had everything under control.
The author uses relatable examples from his own family, and offers several different talking points to work with your child, not to dismiss the fears outright, but to help them work through the fears and conquer them.