Kate Fitzgerald, 12, Hailee Karekare, 11, and Shae Lyons, 11, from Maihiihi School placed second.
Angel Oakley-Smith, 12, Te Koha Martin, 11, and Kate Rye, 11, who are also from Maihiihi School, were third.
All three teams have qualified for the AgriKidsNZ Grand Final in Hawke's Bay.
"It's awesome. We had a great time at last year's event. We are a good team because we help each other out and can work together," said Fladgate.
Both national finals will take place alongside the prestigious FMG Young Farmer of the Year Grand Final in July.
The FMG Junior Young Farmer of the Year competition was formerly known as TeenAg.
Both events are a key part of the work being done by NZ Young Farmers to attract students into the agri-food sector.
Results:
Waikato/Bay of Plenty regional final: FMG Junior Young Farmer of the Year
1st Finn Patterson and Campbell Trousdale. Hauraki Plains College. 2nd Alex West and Alex Fitzgerald. Te Awamutu College. 3rd Chloe Cole and Nerida Bateup. Te Kauwhata College.
1st Quin Farrell, Liam Loijen and Nathan Fladgate. St Mary's Catholic School. Putaruru. 2nd Kate Fitzgerald, Hailee Karekare and Shae Lyons. Maihiihi School. 3rd Angel Oakley-Smith, Te Koha Martin and Kate Rye. Maihiihi School.