Directors of the 600,000-member organization voted by a show of hands to replace first secretary Julio Martinez with Liudmila Alamo, who had been second secretary.
Martinez remains a member of the Council of State, Cuba's supreme governing body, and in the island's rubber-stamp parliament.
Past union leaders include Otto Rivero, who became a vice president, and Carlos Lage, a vice president who was de-facto economic czar. Both were fired in a leadership shake-up in March.
The union is an important recruiting ground for new party members charged with carrying communist ideals into the future.