In 2000, Whatley was a member of George W. Bush's team pursuing the Florida recount. During Bush's presidency, Whatley served in the United States Department of Energy as deputy assistant secretary.[4] In 2004, he became chief of staff for U.S. Senator Elizabeth Dole, replacing Frank Hill.[4][5] In 2007, Whatley became a partner at lobbying firm HBW Resources, and in 2008 he became executive vice president for the Consumer Energy Alliance; he held the position until 2019.[6][7] In 2016, Whatley helped Republican presidential nominee Donald Trump campaign and organize rallies in North Carolina.[6]
Following the United States Capitol attack on January 6, 2021, Whatley refused to blame Trump, saying that only those who participated in the riots bear responsibility.[11][12] In February 2021, Whatley said, "We certainly saw evidence of voting irregularities, of election counting irregularities in a number of places around the country", and that the reason Trump won North Carolina was his state party's vigilance against Democrats' attempts to cheat.[13] Also in February 2021, the state party voted unanimously to censure Senator Richard Burr for voting to convict President Trump during his second impeachment.[14]
The Republican National Committee appointed Whatley as its general counsel in February 2023.[15] In February 2024, Donald Trump endorsed Whatley to replace Ronna McDaniel as chair of the RNC.[16] In March 2024, Whatley was elected as the new chair of the RNC, along with Lara Trump as his co-chair.[17][18] Per the North Carolina party's 2022 plan of organization, its vice chair (Susan Mills) served as state chair until a successor was elected.[19][20]