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Lord (16) won impressively in 23min 42sec, outpacing Otago and national champion Rozie Robinson over the distance in the multigraded field.
He follows in the footsteps of his older brother, Daniel, and hopes to beat Daniel's national secondary schools 3km track walk time (12min 50sec) in Dunedin in two weeks' time.
To gain bragging rights over his brother, Lord needs to better his personal best over the distance by 23sec. An added motivation for doing so is possible selection for the world youth meeting in Sydney in January.
"I have to shine and impress the selectors," he said on Saturday. "That record would help."
Daniel Lord represented New Zealand at the world cup in Mexico and won a junior age-group title at the Pan Pacific championships in Canberra.
Jonathan has three national junior titles and a silver medal in the national junior men's 10km.
He trains six days a week, mixing speed and endurance.
Although outgunned over the first 5km by Lord, Robinson won a third successive Otago 10km title, clocking 53min 22sec.
Robinson has dominated local and national women's competition for the past three years.
Earlier this year, she recorded a personal-best time for 10km of 49min 42sec at the Oceania championshipsin Cairns.
"I knew today wasn't going to be that fast," she said on Saturday, pointing out she was concentrating on endurance training at present. "It was a case of getting a race under my belt to mix in a little bit of speed."
Robinson's next major competition will be a 3km event held in association with the Lovelock Classic meeting in Timaru in early January.
After that, she is targeting a time of about 1hr 40min at the national 20km championships in March, to qualify for the World University Games.
Matthew Ogle made it a threepeat in the boys 14 and under section on Saturday.
Ogle (13), a year 9 pupil at Otago Boys' High School, clinched the title over 2km in a personal-best time of 12min 3sec.
While he, too, may feature at the national secondary schools championships in Dunedin, he is also targeting a third consecutive Colgate Games title in Invercargill in January.