Paul Chan, vice chancellor and president of HELP University in Kuala Lumpur, said the North Korean ambassador accepted the degree on Kim's behalf Oct. 3, The Wall Street Journal reported Thursday.
Chan, in a lengthy statement, said he hoped honoring Kim would help bring closer ties between the secretive regime in North Korea and Malaysia. He described it as a "bridge to reach the people."
Kim, believed to be under 30 when his father, Kim Jong Il died, is little known, although he studied in Switzerland for a time as a teenager.
Malaysia has an embassy in Pyongyang, and the two countries even have an agreement that allows Malaysians to travel to North Korea without visas for stays of no more than 30 days.
Chan said he expects reclusive North Korea to engage the outside world more within the next five to six years. He predicted the country will be a magnet for investors.
"I am just a bit ahead of them in that I feel no one at this moment has the courage to do this, though their hearts tell them to do so," he said.