In what is believed to be the first such incident in Sweden, the 62-year-old died shortly after the incident, which occurred during a junior game near Sollefteå in northern Sweden.
Police said the referee was wearing a helmet but the puck struck a fatal blow when it hit him high on the back of the neck.
"The puck struck the referee between the nape (of the neck) and the lower part of his head, just under where the helmet stops," said Börje Öhman, a police officer in Västernorrland county.
The players in the under 18 game, some of whom were as young as 15, were distraught after the incident.
"They were very upset and wondered what would happen to the boy that shot the puck," one of the team's trainers told the local radio station P4.
Despite efforts to revive him, the referee was pronounced dead before emergency services had reached the hospital.
According to Jörgen Lindgren, the general secretary of the Swedish ice hockey federation, it is the first such ice hockey related death in Sweden.