Four charities withdrew as official partners from the Kiltwalk earlier this year and its chief executive stepped down a few weeks later.
The Kiltwalk stages sponsored walks across Scotland to raise money for leading children's charities.
Its 2013 accounts showed more was spent on costs than went to charity.
There is no suggestions regulations were broken.
Kiltwalk chairman Michael Ure said it had incurred additional costs because of a "re-structuring".
Mr Ure and the rest of the trustees have now stood down.
The Kiltwalk said a new board would oversee the continued development of the charity.
The group has also attracted support from one of Scotland's richest men, the entrepreneur Sir Tom Hunter, whose foundation has committed long-term funding.
Mr Hunter said: "The Kiltwalk is a fantastic concept for raising much-needed funds for Scotland's children's charities and has our absolute support.
"We intend over the next couple of months to redefine and improve the model, building on the foundations already in place, to maximise returns for charities and turbo-charge Scotland's Kiltwalkers for 2016."
The Kiltwalk was set up in 2011 with the aim of bringing Scotland's leading children's charities together for a series of sponsored walks.
It grew from 800 walkers that year to more than 12,000 across the country in 2014.
However, earlier this year four charities - CLIC Sargent, Cash for Kids, Aberlour and Edinburgh's Sick Kids Friends Foundation - withdrew as official partners.
CLIC Sargent and Aberlour indicated to BBC Scotland that they had concerns over the amount of money reaching them from the Kiltwalk.
The most recent set of accounts for the Kiltwalk showed that from an income of just over Â£1.6m, Â£780,000 had been spent on running costs - more than the Â£776,000 which went to charity.
A Scottish charity has replaced its entire board of trustees following concerns over the amount of money it was giving to charitable causes.