Why does baby wake up crying? Obviously, a baby wakes up crying to eat, because they are wet or dirty, or to have their sleep association recreated (such as replacing a pacifier). But, what does it mean when your baby wakes up crying from a nap, or in the morning when they are "done" sleeping? Baby Crying Between Sleep Cycles Unfortunately, there doesn't seem to be a definitive reason as to why a baby wakes up crying. However, it is normal for them to cry between sleep cycles.