To celebrate the milestone the school received a bonus package of Chromebooks, which the students quickly put to use, working on self-directed learning projects during their "Genius Hour".
Principal of Clutha Valley School, Val Ward said the "Fuel for Schools" programme was "a fantastic initiative".
"It's given equitable access to children in our school with the Chromebooks" Ward said.
Southfuels customer Hannah Harwood said it was great to know that the money from her fuel purchase was going back to rural kids.
"We love buying our fuel from Southfuels because they give so much back to the community".
Southfuels Chief Executive Bryan Jamison delivered the one-thousandth $1000 cheque to Clutha Valley School in person.
He said Southfuels was "extremely proud" of the programme and all it had achieved for rural schools so far.
"Our Fuel For Schools programme ... has donated over a million dollars to 350 schools across New Zealand in rural communities".
Find out more about Southfuels' Fuel for Schools programme here.