The organisation's CEO Andy Hawthorne also picked up the best leader award at a ceremony in London.
The Message was founded in Manchester with the intention of sharing the Christian message in schools, prisons and tough communities across the UK.
Speaking to Premier, Andy Hawthorne said he was humbled and honoured to be recognised for the work.
"It's a privilege to be voted one of the top 100 charities in the UK and then to come runner-up against all these amazing charities and then for me to win this leader's award was the icing on the cake," he said.
Now in its 25th year, The Message Trust operates in deprived areas of the UK. It sends missionaries to live locally among the people and build authentic relationships with the people there.
"Every team is changing the community - not just growing the church - but the community is getting better, health is getting better, education, people are earning more money and living better lives.
"It's God who's doing it, through his people and that sort of stuff is starting to get attention and that's what happened last night.
"Life is short and we all have one chance to reach out to hurting people who don't know Christ and show acts of kindness on his behalf. You won't get that chance in heaven so let's get on with that now."
Listen to Marcus Jones speaking to Andy Hawthorne here: