The cruel thieves broke into Hillpark Secondary School in Glasgow on 23 September and stole £2,000 from the safe.
The pupils had been working tirelessly to raise the cash for the 'life-changing' charity work in the African country.
RAD MORE: Last-ditch bid to halt Scotland smacking ban as MSPs prepare to pass lawThe money had been raised through a tombola, raffle, face painting and race night.
A GoFundMe page has since been set up by pupils and staff hoping to make up for the money lost.
Around £600 has been raised in the space of five days, but pupils say they're devastated at having to start from scratch.
One of the pupils, Rachel Waugh, said: "We're devastated, it's really quite a shame.
"We worked so hard to raise that money over and above what we all need to raise individually.
"Every weekend we've been out doing fundraisers, tombolas, anything we can do to raise the money.
"We're up before people are even awake to set up, and for that all to be wasted and have to start again is disappointing to say the least.
"It's just disgusting. I don't understand why they would do it.
"I think it's really unfair and cruel."
He added: "I spent months organising a race night on the Friday night and it went really well, and for it all to be stolen by the Monday is really sad.
"This is affecting people on the other side of the world, it's not really fair.
"It's really sad that we've put so much effort into that and it's all been put to waste.
"It's just frustrating."
A Glasgow City Council spokesman said: "The young people have worked so hard to raise the valuable funds for their Malawi project and are devastated at the mindless acts of vandalism and criminal activity.
"They held a very successful charity event that was hosted by pupils in the weekend prior and money was secured in the school safe.
"Anyone with any information about the break in should contact the police."
A Police Scotland spokesman confirmed they were aware of the incident and enquiries were ongoing.
Anyone with information is urged to call police via 101.
To donate to the fundraiser visit https://www.gofundme.com/f/yfp9t-malawi-project?fbclid=IwAR2oWdVLJkeXOjhEwNC0PCQofb4OcoHOMUB_7fw4lDDpzGZbHFMadjbuGB8.