Former head of NYSE Euronext, from December Mr Thain will attempt to help Merrill Lynch get back on track after it revealed enormous credit crunch-related losses.
Citigroup had been expecting to entice Mr Thain, but their loss will be Merrill Lynches' gain, with the man's 20 years of experience at Goldman Sachs, in both mortgage bond trading and president.
Mr Thain's last role was at NYSE role, where he has presided since January 2004 and achieved the transformation of the Big Board from a domestic organisation into a global bourse as well as master-minding the firm's new automated trading system.
The 52-year-old has been replaced at NYSE Euronext by Duncan Niederauer, president and co-chief operating officer of the organisation.
Merrill Lynch is committed to repairing its reputation after the largest quarterly loss in its 93-year history of $2.2 billion for the third quarter and a $8.4 billion writedown due to the US sub-prime crisis.
Mr Thain's appointment was a surprise since experts touted Larry Fink, the chief executive of BlackRock, for the job.