The resignation of Hiroharu Kitani was confirmed by the Science and Technology Agency. The company, JCO Co., did not answer calls late Friday.
The Sept. 30 accident at the uranium-processing plant in Tokaimura, 70 miles northeast of Tokyo, killed one plant worker, seriously injured two other workers and exposed more than 400 people to radiation.
The accident shook the public's faith in the safety of Japan's nuclear power program. Workers who ignored safety regulations while mixing nitric acid and highly enriched uranium set off an uncontrolled atomic reaction that went on for hours.
Kyodo News agency quotes Kitani as saying JCO will continue to exist as a company while it compensates the victims and deals with health concerns.
The government has repealed JCO's operating license, so it is no longer processing fuel.
Moriki Aoyagi, president of Sumitomo Metal Mining Co., which owns JCO, stepped down earlier in February.