Kobayashi put away 49 hot dogs in 12 minutes, using a new technique known as "the three-way" that involves downing three dogs at a time, the New York Post reports. His impressive total was four and a half dogs short of his personal best.
Kobayashi, who was carried into the contest area on a platform decorated with hot dogs, took home the mustard yellow champion's belt once more after winning the 90th Nathan's July 4th contest.
The Japanese have dominated the Nathan's event in recent years, winning the last eight championships. The runner-up and American record-holder, Sonya Thompson, broke her own record with 37, while a newcomer, Joey Chestnut, came in third with 32.
Kobayashi had said he would retire if he set a new record.
"I will be back next year," he promised after he fell short.