[4] The 1998 marathon established a new course, starting at Tsing Ma Bridge and ending at the newly finished Hong Kong International Airport on Chek Lap Kok.

In 1999, the race was moved to urban areas for the first time, starting in Central, ending at Sham Shui Po Sports Ground, with 7,000 participants.

The route was altered again in 2000, as it started from Hong Kong Cultural Centre, Tsim Sha Tsui, and ended at the Sham Shui Po Sports Ground.

The racecourse started from Nathan Road, then out to West Kowloon, onto West Kowloon Highway, followed by Cheung Tsing Tunnel, Tsing Ma Bridge, Ting Kau Bridge, then going all the way back into Western Harbour Crossing, ending at Golden Bauhinia Plaza in Wan Chai North.

Due to the proximity of Island Eastern Corridor from residential blocks such as those at City Garden, and also the early starting time of the races (05:10 to 06:40), residents complained about noises as loud as 60dB.

The organizer, however, stated that it hopes to use IEC again for the 2009 Marathon since it successfully alleviated the problem of large numbers of runners rushing into Western Harbour Crossing, which made breathing difficult within the tunnel.

[9][10][11] The full and half marathon's race tracks remained generally the same, starting from Nathan Road, Tsim Sha Tsui, then going out to West Kowloon using Austin Road, followed by West Kowloon Highway and Tsing Kwai Highway, where half-marathoners turn back.

Competitors then ran back all the way to West Kowloon, joining half-marathoners again at Kwai Chung, and into Western Harbour Crossing.

Japanese runner Koichioro Fukuoka won the full marathon in 2:16:50, ending Kenya's four-year domination of the event.

[4] At the 2011 edition, held on 20 February, Nelson Kirwa Rotich won the men's elite race in a time of 2:16.00 hours.

The move paid off as she won the race in a new women's course record time of 2:33:42, erasing Irina Bogachova's ten-year-old mark.

[20] The second fatality in the competition's history occurred that year, when a 26-year-old male half marathon runner fell unconscious after he passed the finish line, and announced dead after he was sent to hospital.

[23] A 24-year-old male Ng Cheuk-yue from the 2015 race died of an unknown cause in a hospital after a heart attack[24] and then head injury just one hundred metres away from the finish line.

[25][26] Ethiopian runner Sentayehu Merga Ejigu won the men's race with two hours, thirteen minutes, and forty-six seconds; North Korean runner Kim Hye-gyong won the woman's race with two hours, thirty-one minutes, and forty-six seconds.

[36] Wong won by four seconds in his debut marathon, which he ran against the advice of his doctors, after having taken two years to recover from a serious knee injury.

[36] As this was the first edition of the race held since the pandemic began, the number of participants was reduced by about 75 percent, and no overseas runners were invited.

[43] The marathon begins on Nathan Road in Tsim Sha Tsui, crosses Stonecutters and Ting Kau Bridges, then runs through Cheung Tsing and Western Harbour Tunnels before finishing in Victoria Park.