Yoon Young-kwan tendered his resignation in response to accusations from President Roh Moo-Hyun that officials in the foreign ministry were blocking his policies.
"Foreign Minister Yoon offered his resignation and President Roh accepted it," a presidential aide said.
The president had at a press conference on Wednesday publicly criticised officials at the ministry and said he was preparing a reshuffle to replace them.
"These officials will be replaced so there will no longer be obstacle to pursuing my foreign policy," Roh said.
A dispute between the president and the foreign minister erupted last year when senior diplomats were reported to have disparaged Roh's advisers on foreign policy.
The presidential advisers in turn were said to have criticised the diplomats as being too pro-American.
Foreign ministry officials apparently want to maintain traditional close ties with the US. Roh, however, says South Korea should never "kowtow" to the US.