The Children's Food Trust, has cited difficulties caused by the "political and economic climate" for the decision to close its doors. It was first launched by government in 2005 in response to a campaign led by celebrity chef Jamie Oliver around the poor quality of school meals.
The decision to close it comes four years after the Department for Education announced it was cutting its funding for the charity.
Originally called the School Food Trust it became a charity in 2007. Its work has included launching national school food standards and creating the Let's Get Cooking network of around 5,000 cooking clubs.
"Given the political and economic climate all charities are facing difficulties and we are no different," Linda Cregan, chief executive of the Children's Food Trust, said.
We remain passionate and dedicated to improving child health but it has proved impossible to continue to deliver our services and, extremely reluctantly, the trustees have chosen to close the trust,"
"It is our priority at this point to speak to all our funders and partners to ensure a smooth transition and a positive legacy.
"We are all very proud of the contribution we have made to the real positive differences in child health in the UK."
The charity's chair of trustees Adam Starkey called on the government, the food industry and retailers to ensure they continue the charity's work and invest in improving children's health.
"We still face a crisis in child health, now more than ever, work in this area is vital, he said," said Starkey.
"We urge everybody to ensure that action to improve children's diet and the standard of the food they eat does not lose pace. Government, food producers and food retailers must make a commitment to researching what works, creating approaches and policies that have an impact, and campaigning to change behaviours that get children to eat well."
The charity's other work included developing food and drink guidelines for early years providers in 2012. Last year it was commissioned by Public Health England to develop revised menus for early years settings as part of the government's childhood obesity plan.
Neil Leitch, chief executive of the Pre-school Learning Alliance, praised the charity's support of the early years sector to help improve children's diet and health.
"We are saddened to learn the news that the Children's Food Trust is to close its doors," Leitch said.
"The alliance has been involved with the trust for a number of years and has always supported the organisation's excellent work improving the wellbeing of children in the early years.
"The loss of this charity will be keenly felt by colleagues across the sector. However, the collective drive and passion of all those who worked for the Children's Food Trust will having a lasting, positive effect on children's health in the United Kingdom and the organisation's legacy should not be underestimated."
The trust was set up with a £15m grant from the then Department for Education and Skills and in 2007 it secured £20m of Big Lottery funding to set up the Let's Get Cooking initiative.