The National ME Centre, a registered charity based in Romford, Essex, will either suspend operations for three months or close down permanently unless it can raise between £30,000 and £40,000.
Karen Walsh, manager of the centre, said that since the tsunami happened the charity had struggled to raise enough funds to supplement the charges paid by patients or primary care trusts.
"Fundraising has become extremely difficult across the board, particularly for something that isn't a high-profile condition," she said. "Our funding has always been vulnerable, but over the past 18 months things have become quite serious."
The centre has been running for 16 years and has helped more than 10,000 patients.