Transforming Lives for Good (TLG) topped a list of one hundred groups, compiled by the Sunday Times.
The children's charity - with the support of local churches, runs holiday lunch clubs and helps youngsters with mental health problems.
Emily Alty, TLG's Head of People and Culture told Premier the company is delighted.
Speaking during News Hour, she said: "We really feel God's blessed us with a great team, united in our mission to help churches to support struggling children.
"Knowing that our team loves working at TLG makes this so special."
The Sunday Times' list of 100 best not-for-profit organisations to work for in 2019 accepted submissions from thousands of companies from across the UK to "showcase the very best in workplace engagement".
TLG, led by founder Tim Morfin has also been awarded a three-star accreditation by Best Companies, recognising the highest level of workplace engagement.
Morfin said: "It's an incredible honour to top the list of the best charity employers in the UK.
"It's amazing to have witnessed this organisation grow and see the impact that TLG is having through local churches in the lives of struggling children and families."
TLG has spent more than 20 years on the frontline supporting children and young people needing support in the school system.
With 13 alternative provision education centres across England and 214 volunteer-led programmes in operation across the UK, TLG seeks positive outcomes for children in some of the most difficult circumstances.
Listen to Emily Alty speaking to Premier's Eno Adeogun:
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