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Greene (17), who is coached by Jim Baird, led from the start and increased her lead throughout the race to win by the big margin of 56sec, in a time of 13min 43sec.
Jaye Atkin (Rangiora) was second in 14min 39sec and Shauna Pali (Kavanagh College) third in 14min 44sec.
Atkin and Pali had a close battle with Atkin just having an edge of speed at the end.
Laura Carruthers (Columba College) was eighth in 15min.
Greene, who left for Europe with the New Zealand Development team yesterday, was a key member of the St Hilda's team that finished third in the six-girl senior teams race.
The other scoring runners were Caitlin O'Brien 18th, Ruby Smith 48th, Virginia Wilson 62nd, Mary Smith 64th and Ellen O'Connell 74th.
The event was won by Wanganui Collegiate with 166 points, from New Plymouth Girls' High School 177, and St Hilda's 267.
St Hilda's also finished third in the junior girls teams race, with Harriet Keown 36th, Meg McKay 39th, Maddy McAlister 50th, Millie Gordon 55th, Holly Campbell 83rd and Esther Fogarty 86th.
Nikita White (Otago Girls') was first in the girls AWD race in 10min 28sec and David White (King's) won the boys AWD title in 7min 20sec. Both events were over 2km.
Tim Morrison (Kavanagh College) was fifth in the Year 9 race, in 10min 03sec over 3km.
Joshua Browne (John McGlashan) was sixth in the junior boys race over 4km, in 13min 20sec.