Huh Jung-moo, vice president of the Korea Football Association (KFA), the country's football governing body, also stepped down.
South Korea failed to advance to the round of 16 as it went winless in matches in Group H, its worst World Cup performance since 1998.
“I’m resigning from the job to take responsibility (for the poor results). I’ll make efforts to develop myself further,” coach Hong said in a news conference at the KFA office in central Seoul. He assumed the post on June 24 last year.
Hong's resignation came a week after the KFA retained Hong despite mounting criticism on the country’s first winless World Cup in 16 years.
South Korea finished the tournament last in Group H with a draw and two losses.