The 17-year-old Johor swimmer clocked 1:02.56 at the Bukit Jalil Aquatic Centre to beat Elvin’s mark of 1:02.59 set in 2000.
Hong Kong’s Kwok Ka Fai picked up the silver with a time of 1:03.87 while Selangor’s Daniel Lim clocked 1:03.92 to take the bronze.
“It’s an unbelievable feat ... it still hasn’t sunk in yet,” said Fu Kang.
“I have been training very hard for the past four months but I didn’t expect to break the national record,” he added.
Fu Kang’s efforts earned him a ticket to the Singapore SEA Games in June and the World Championships in Kazan, Russia, in July.
He attributed his success to the training programme at the British International School in Phuket, Thailand, where he has been studying for the past six months.
“The training there is more organised and I have benefited from it,” said Fu Kang.
Fu Kang is now all fired up to increase his gold tally. He will compete in the 50m breaststroke and 200m individual medley.