MUFG Securities EMEA plc, the European investment banking unit of MUFG, currently has its head office in London with staff of about 600 people.
"The new subsidiary in Amsterdam will ensure that the Group can continue to provide these (securities) services to its EU clients, even if the cross-border passport is lost as a result of Brexit," MUFG, which has $2.8 trillion in assets, said in a statement on Wednesday.
The timing of the start of Amsterdam operations is undecided since it is subject to approval by authorities, the bank said.
MUFG also said it plans to open an investment banking branch in Paris and that several dozen people will be moved from London to either Amsterdam or Paris. The bank has already picked the Dutch city as its commercial banking operations hub in continental Europe.
Global banks have said they could move thousands of jobs out of Britain to prepare for Brexit, the country's planned exit from the European Union in 2019.
MUFG's choice of Amsterdam as its EU hub, however, bucks the trend of other Japanese and global banking peers.