The modules tested the pupils' practical and theoretical skills and included a quiz hosted by Te Radar.
Both the first and second-placed teams qualified for the Junior Young Farmer of the Year grand final in Hawke's Bay in July.
Cooper Mitchell, Ben Cairns and Danny McDonald from Limehills School, near Winton, won the AgriKids NZ contest.
They were among 144 pupils, working in teams of three, who tackled a series of eight fun modules and the top seven teams went head-to-head in a race-off.
Competition co-ordinator Jake Lonergan said the aim of the event was to get children excited about the opportunities in primary industries.
Chonelle Ayson, Jessie McFadzien and Hanna Lawlor, from Longford Intermediate School in Gore, were second and Archie Chittock, Flynn Hill and Shamus Young, from Blue Mountain College in Tapanui, were third. All three teams have qualified for the AgriKids NZ grand final in Hawke's Bay.