Hierro was placed in interim charge of the 2010 world champions following the dismissal of Julen Lopetegui, who accepted the Real Madrid job without correctly informing the RFEF.
La Roja progressed through the group stage of the tournament, but lost on penalties to hosts Russia in the last-16 stage of the competition.
Hierro had previously been in the role of sports director at the RFEF, but has now severed all ties.
"The Royal Spanish Football Federation and Fernando Hierro put an end to their relationship once the participation of Spain in the World Cup in Russia ended," read a statement from the RFEF.
"He declined to return to his previous position as sports director of the RFEF to seek new horizons and undertake new professional challenges."
Spain will begin their qualification campaign for Euro 2020 in September.