The charity, based in Winchester, learnt of their win during a surprise visit from musician and entrepreneur Tinchy Stryder, who presented the prestigious prize, during a workshop run by 23-year-old Fixer Chelsey Jay.
Chelsey, who's campaigning for disabled people to be better represented in the media, was left stunned, but delighted.
She said: "It's been an emotional whirlwind - it's been absolutely mental. I'm just filled with so much pride. Fixers is in my heart as they've changed my life. Having them recognised is just beautiful."
Originally selected from over 750 award entries, Fixers fended off tough competition from six other finalists in their category, as the charity received 6,919 votes to claim the top spot.
After making the announcement, Tinchy Stryder was full of praise for Chelsey and the other young people that Fixers are enabling to make positive change.
He said: "Fixers is something that gives them the opportunity to have their voices heard. It felt great to present the award. When I arrived I knew a bit about the charity, but now I've learnt so much more. It's opened my mind.
"It feels good to see that people are using their experiences of certain issues to help others across the UK. It's from the heart, and that's what I love about it."
The awards are an annual search to find the UK's favourite Lottery-funded projects and they aim to recognise the difference those initiatives have made across the nation.
Margo Horsley, Chief Executive of Fixers, said: "There are 13,200 Fixers UK-wide and this award recognises their courage and contribution to society.
"Fixers have different backgrounds, interests and life experiences, and come from every corner of the UK.
"But they do have one important thing in common. They use their past experiences to shape a bigger and better future for everyone. Every single one of our Fixers should take pride in winning this award. It is recognition for all their hard work and their belief in making a positive difference."
Winchester & Chandler's Ford MP Steve Brine added: "I am thrilled to hear about the award, and also the manner in which they found out! I've been a strong supporter of Fixers throughout my time as the MP, both in Parliament and here in Winchester, and a huge well done to them all."
Fixers' achievement will be celebrated at a special, televised ceremony later this month, and you can watch 'The National Lottery Stars' at 10.30pm on Friday 19th September on BBC One.
Pictured; Tinchy Stryder joins the Fixers
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ITV News Meridian also featured the presentation in their evening programme on Tuesday 2nd September.