Fred Phelps was born in Meridian, Mississippi in 1929, the first of two children; his sister, Martha-Jean, was one year younger. His father, Fred Wade Phelps, was a "bull" employed by the local railroad, whose job was to keep people from illegally riding the rails. Fred recalls his father often came home from work "with blood up to his shoulders". Fred's mother, Catherine Phelps, was a homemaker.

The family were devout members of the Methodist Episcopal Church, South. Catherine died of throat cancer at the age of twenty-eight, when Phelps was five years old. It was the first significant experience of his life, and one that appears to have affected him greatly. One of Fred's only memories of his mother is the fact that since she was the only woman on their street who owned a musical instrument (a piano), she used to push it to the front of the house, open all the doors and windows, and play for the pleasure of the neighbors. Catherine was highly regarded in Meridian — her funeral was attended by the mayor (who was also a pallbearer), a city councilman, two judges, and every member of the Meridian police force.[9]

Shortly after his mother's death, his maternal great-aunt, Irene Jordan, moved in with the family and became a surrogate mother; she was killed in a motor vehicle accident in 1950, shortly before Fred's twenty-first birthday.[9]

Friends and enemies alike recall the young Fred Phelps as a bright, quiet young man; those asked seem to unanimously agree that he was fairly well liked in high school, despite not being very sociable (something to which Phelps himself admits). Friends further recall that Phelps had tendencies to be overbearing and arrogant. By Phelps's own admission, he never dated, and had no interest in members of the opposite sex. He played in the school band (cornet, later switching to bass horn), was on the track team (he specialized in hurdling), and worked as a field reporter for the high school newspaper. Also, during his time in high school he became a Golden Gloves boxer, going to state twice and winning by KO both times. In his graduation-year yearbook, his classmates predicted that he would end up as a professional boxer.[9]

In 1947, Phelps enrolled as a student in at fundamentalist Bob Jones University, which he left after three semesters.[10] He then spent two semesters at the Prairie Bible Institute. In 1951, he earned a two-year degree from John Muir College.[11]