The parliamentary bill creating the Financial Intelligence Authority was passed in July 2013, after two previous attempts. Known as the Anti-Money Laundering Act, the law aligns Uganda with its East African Community neighbors—Kenya, Tanzania, and Rwanda—which had enacted similar legislation earlier.The objectives of the Authority are to:Enhance the identification of the proceeds of crime and the combating of money laundering,Ensure compliance with this Act,Increase public awareness and understanding of issues related to money laundering,Make information it collects available to competent authorities,Facilitate the administration and enforcement of the laws of Uganda, andExchange information with similar bodies in countries that have treaties, agreements, or arrangements with the Government of Uganda regarding money laundering and related offenses.

In July 2014, Ms. Maria Kiwanuka, Uganda's then Finance Minister, appointed Mr. Sydney Asubo, an experienced lawyer, as the interim Executive Director for six months while the agency's Board of Directors was being constituted.

During the financial year 2017/18, Cabinet expanded the mandate of the FIA by directing it to support MDAs in conducting financial and integrity due diligence on private companies intending to partner with the Government to implement infrastructure development under a Public-Private Partnership (PPP) framework. The intention is to mitigate the risk of partnering with foreign investors who may be potential fraudsters.