Before taking on her position in the Bush Administration, Frazer was special assistant to the president and senior director for African affairs on the National Security Council and the first woman to serve as United States Ambassador to South Africa.

Frazer is also given credit for designing the administration's policy for ending the wars in the Democratic Republic of the Congo, Sierra Leone, Liberia, and Burundi.

[5][6] John Bolton, the Bush Administration's Ambassador to the United Nations, accused Frazer of setting back his plans to end the U.N. Mission in Eritrea-Ethiopia that monitored and acted as an interposition force along the disputed border between Ethiopia and Eritrea by unilaterally deciding that the 2002 decision of the Ethiopian-Eritrean Boundary Commission should be cast aside to favor Ethiopia's position.

Frazer has also been accused[8] of quietly encouraging Ethiopia's decision to militarily intervene in Somalia in late 2006, a contradiction of the administration's official position.

[13] On April 24, 2008, Frazer noted that Zimbabwe opposition leader Morgan Tsvangirai of the Movement for Democratic Change won the disputed Zimbabwean presidential election, 2008, and stated that President Robert Mugabe should step down.

[14] On May 25, 2008, Mugabe delivered a speech that mentioned Frazer in negative terms: "You saw the joy that the British had, that the Americans had, and saw them here through their representatives celebrating and acting as if we [Zimbabwe] are either an extension of Britain or ... America.

You saw that little American girl [Frazer] trotting around the globe like a prostitute ..."[15] As of late October 2008, she has been put in charge of issues concerning the Conflict in North Kivu.

[16] On August 8, 2016, Frazer became one of fifty senior national security and government experts to sign a letter highly critical of the Republican candidate for the 2016 US presidential election, Donald Trump.