The loss is equivalent to just under £3.5m.
“This breach represents a small fraction of Bitstamp’s total bitcoin reserves, the overwhelming majority of which are held in secure offline cold storage systems,” Bitstamp said.
“We are working to transfer a secure backup of the Bitstamp site on to a new safe environment and will be bringing this online in the coming days.”
Bitstamp’s services wil remain suspended while the firm investigates the breach.
In February 2014, exchange Mt. Gox closed down after a theft of Bitcoin worth £280m at the time. It eventually filed for bankruptcy.
Shai Heffetz, the chief executive of brokers InterTrader, said that ongoing setbacks were unlikely to lose Bitcoin popularity.
“This latest blow doesn’t mean Bitcoin will go away anytime soon. Even without the backing of regulation, digital currencies are increasingly gaining favour with those who realise the benefits of side-tracking traditional currencies,” Heffetz said.