The Shine On campaign was started by Ryan McLaughlin when he was 14 to raise awareness of the role vitamin D supplements can play in preventing the spread of MS.
Ryan was inspired after his mother Kirsten, a former taekwondo champion, fell ill with the disease.
However, after three years of fighting to change official thinking and get the Scottish Government to provide free vitamin D to schoolchildren and pregnant women, funds have now run dry.
The campaign's website was briefly taken down this week as they could no longer afford internet charges, and much of the data they had collected on the importance of vitamin D was lost.
The campaign's manager, Alan McLaughlin, Ryan's father, said: "We ran out of everything a couple of weeks ago and the website had to be taken down. We lost everything – about 700 pages of information and links we had collected to help the appeal and tell people about vitamin D.
"We've been running the campaign from home and speaking to people in Australia, the US and Canada, and that has meant our phone bills have been high day-to-day.
"So, with those costs and the website, our funds have just dried up. We'd hoped to get help from other charities but it's not been forthcoming."
Mr McLaughlin and his son scored noticeable successes when they led a march of hundreds of Saltire-waving children down the Royal Mile in Edinburgh to deliver a petition to the Scottish Parliament.
Pressure from the campaign also encouraged Health Secretary Nicola Sturgeon to agree to a summit to raise awareness of the impact of vitamin D on MS, and to issue fresh information based on the research they had collated.
The McLaughlins' campaign saw Ryan nominated for The Herald's Campaigner of the Year and also honoured by the Multiple Sclerosis Society.
Many scientists believe that MS is directly linked to vitamin D deficiency. The muscle- wasting disease has no cure and affects 12,500 Scots, the highest rate of any country in the world.
Vitamin D is known as the "sunlight vitamin" as it comes from sunshine, and one theory about why MS is so prevalent in Scotland is that it is linked to dark winters north of the Border.
Mr McLaughlin said they had been struggling to keep the campaign going for a while after his wife's condition worsened and she began to require more care. Ryan, who is now 16, is also studying for his exams.
However, his father said they intend to keep going as long as they can, and have set a new fundraising target of £3000 to keep the effort going.
He said: "We considered calling it a day when the website went down, but we got lots of emails from people supporting us, and we don't want to let people down.
"People have been urging us to fight on, so that's what we're going to do."