The song is about the Moors murders that took place on Saddleworth Moor, which overlooks Manchester, between 1963 and 1965. At the time of their deaths, many of the victims were only a few years older than Morrissey (born 1959), who wrote the lyrics of the song after reading a book about the murders, Beyond Belief: A Chronicle of Murder and its Detection by Emlyn Williams.
"Suffer Little Children" was one of the first songs that Morrissey and Johnny Marr wrote together.
The title of the song is a phrase found in the Gospel of Matthew, chapter 19, verse 14, in which Jesus rebukes his disciples for turning away a group of children and says:
Although five children were murdered in the Moors murders case, only three are named in the song: John Kilbride ("oh John you'll never be a man"), Lesley Ann Downey ("Lesley Ann with your pretty white beads"), and Edward Evans ("Edward, see those alluring lights"). The murders of Keith Bennett and Pauline Reade were not attributed to Myra Hindley and Ian Brady until 1985, after "Suffer Little Children" had already been released.