Graduated in 2000 from the Faculty of Law of the University of Lisbon and in 2002 completed the European Master's in Human Rights and Democratisation (E.MA) at the European Inter University Centre for Human Rights and Democratisation. She practised law for 17 years in the areas of criminal litigation, administrative offences and compliance.
Since 2019, Filipa Marques Júnior has been Deputy Director of Banco de Portugal's Investigation and Sanctioning Department, with particular responsibilities in the areas of preventive supervision of money laundering and terrorist financing.