Not including para or masters records, it was the first record set on the track since it was replaced at the end of last season.
The King's High School pupil crossed the line in 39.25sec to shave 0.15sec from his Otago men's 17 years record, which he clocked in February.
McDonald, one of Otago's top medal prospects at the national secondary schools track and field championships in Timaru next month, finished 6.01sec ahead of second placed Jordan Mitchell to win the 15 17 years race.
The Taieri athlete was also too good for 23 year old Hill City-University hurdler Stephen Issac, who clocked 40.43sec.
McDonald, who competed at the Commonwealth Youth Games in Samoa in September, also chalked up a win in the long jump, thanks to a 6.4m effort on his first attempt.
Jackson Stewart (15), one of a bunch of Southland athletes competing in Dunedin at the weekend, was second (5.92m).
Impressive masters runner Myrtle Rough (75) chalked up her third national record in the past month.
Having already set records in the 800m and 1500m in the 75-79 years section, Rough crossed the line in 14min 47.97sec in the 3000m.
Tony Tan (49) set an Otago masters record for men aged 45-49 in the 100m.
The Hill City-University sprinter stopped the clock in 12.64sec, which was not far off what many of the much more youthful runners were doing.
Jessie Murphy recorded the fastest women's 3000m time (11min 12.16sec) of the day, as she won the 15-17 years race.
Fellow Hill City-University runner Anna Lindsay (17) was second in 11min 14.04sec.
Invercargill's Jordan Rackham (19) produced a sharp run to beat out Winton's Jack Beaumont (18) in an absorbing contest in the 18-19 years 3000m.
Rackham had to work hard for it, but crossed the line in a few seconds ahead of Beaumont for the win.
Hill City-University's Oli Chignell opted against running his favoured 3000m, instead looking to increase his speed by running the 800m.
The 17 year old, who is coming off a stellar cross country season, went under 2min for the first time in the two lap race.
He won the 15-17 years race, beating out the nine strong field in 1min 59.60sec.
Matthew Ogle, of Hill City-University, was second in 2min 1.25sec, while Southlander Liam Cullen was just 0.31sec back in third.
Among other highlights on the day
• Hugh McLeod-Jones won the men's 15-17 years discus (45.93m) and shot put (14.31m).
• Ariki's Rory O'Neill beat out Invercargill sprinters Sam Stewart and Josh Correrr to win the 18-19 years 100m in 11.37sec. O'Neill also edged Stewart by 0.97sec to win the 200m.
• Taieri's Joccoaa Palmer won a thrilling women's 15-17 years 200m in 26.49sec. Ellie Duncan, of Hill City-University, was second in 26.64sec.
• Taieri's Christina Ashton won the women's 18-19 years 60m (8.05sec), 100m (12.71sec) and 200m (25.95sec).
• Hill City-University's Caitlyn George won the women's 15-17 years 100m (13.11sec) and 200m (26.51sec).
