The total exceeded the previous record of 19.3 billion won raised by the South's Red Cross over four months to help Americans hit by Hurricane Katrina in 2005, the humanitarian body said.
The March 11 quake and tsunami sparked an outpouring of sympathy in neighbouring South Korea, with many companies and entertainers popular in Japan joining individuals in the rush to donate.
Actor Bae Yong-Joon, who gained fame in Japan with the hit TV show "Winter Sonata", donated one billion won earlier this month.
A Red Cross spokesman said major donations from companies and other institutions, particularly those with strong ties to Japan, helped swell the amount.
Individuals may have felt compelled to help due to the South's cultural links to its neighbour, he said.