The settlement comes after a lengthy investigation into how RBS breached sanctions through illegal transactions with Iran, Sudan, Burma and Cuba.
Criminal authorities at the US Justice Department and the District Attorney of New York have closed their related investigations and will not bring charges, RBS said.
From 2005 to 2009, the bank removed references to sanctioned locations from payment messages to US financial institutions, the Treasury Department said.
RBS instructed employees to list the name of the Iranian financial institution rather than its identifying codes on wire transfers. This prevented the bank's payment system from automatically including references to Iran in the cover messages sent to US clearing banks.
Several UK banks have entered into settlements in recent years over continuing financial transactions with Iran despite US laws against them, and for removing information from payments to get them processed.
RBS said in a statement: "We have today reached a settlement with the Board of Governors of the Federal Reserve System ("Fed"), the New York State Department of Financial Services ("DFS"), and the Office of Foreign Assets Control ("OFAC") with respect to RBS plc's historical compliance with US economic sanction regulations outside the United States.
"The settlement arises from an investigation initiated by RBS plc in 2010 into its historical US dollar payment practices and controls in the UK. This review was shared with the relevant US Authorities in 2010 and has been disclosed in regulatory filings since. The US Department of Justice and the District Attorney of New York have concluded their parallel criminal investigations and are not taking action against RBS plc.
"In settlement with the above Authorities, RBS plc has agreed to pay $100 million (£62 million) in total, with $50 million (£31 million) to the Fed, of which $33 million (£20 million) is deemed to satisfy the OFAC penalty, and $50 million (£31 million) to DFS. This has been fully provisioned.
"RBS plc has cooperated fully with the US Authorities and acknowledges and deeply regrets these failings. RBS plc embarked on an extensive remediation plan to address the shortcomings identified in its investigation. RBS plc has committed almost £300 million (since 2010) to strengthen the bank's control environment on sanctions."
It added that, since 2009, RBS had:
* Instituted a new more comprehensive global OFAC compliance policy with clear guidance including a zero-tolerance for breaches of sanctions requirements and the introduction of electronic filtering of payments including an enhanced filtering approach for Her Majesty's Treasury and OFAC, which goes beyond that mandated by law.
* Conducted an extensive review of all customer relationships in the relevant countries and exited a number of customer relationships.
* Enhanced its Anti-Money Laundering and Sanctions Compliance function and increased its team by more than 730 employees since June 2011 to a total of 1,700 today.
* Strengthened governance at a number of different levels within Group plc to ensure the appropriate coordination and prioritization of sanctions compliance activity across Group plc.
* Instituted compulsory annual sanctions compliance training for all 120,300 employees globally.
Meanwhile, in London, RBS shares took a tumble after the surprise decision by finance director Nathan Bostock to quit the group just two months into the role.
RBS fell 3% after Mr Bostock told the state-backed bank's board he was leaving to join Santander UK as its chief risk officer and deputy chief executive.
His departure came as another blow to long-suffering investors, with the group among the top blue-chip fallers, down 9.8p to 326.9p.