The central character in "They Cage the Animals at Night" is the author, Jennings Michael Burch. Burch was abandoned by his mother when he was eight years old, and the book is his story of his years in foster care and institutions.
Burch is a resilient young boy who quickly learns the hard rules of survival as he is shuttled from home to home. The only constant in his life is a stuffed animal he calls Doggie.
Other characters in the book are his mother, Rita Catherine Hogan Burch, and his siblings, older brothers Larry, George, and Walter, and baby brother Gene. There is also another brother, Jerome, who is not well and spends a lot of time in the hospital. Burch develops a relationship of sorts with Jerome, who attempts to "explain family relationships and the harsh realities of life to him". Burch's time with his family is fraught with difficulties, and when his mother becomes ill, the family is broken up again.
Burch spends time in a series of foster homes, and meets a variety of people in them, some helpful and others abusive. He is befriended by Martha, the cook in one of these homes, and finally crosses paths with Sal, a city busdriver who provides him with the home and support for which he has always yearned.