Thune will lead the Senate Republican Policy Committee, the No. 4 position in the leadership, and play a role in shaping the Republican message and agenda on health care, climate change and spending.
"We're in a bit of a hole but we're going to dig our way out of it," said Thune, who had served as vice chairman of the conference, the No. 5 leadership job. Republicans elected Alaska Sen. Lisa Murkowski to that post.
Democrats currently control 59 votes in the Senate and hope Al Franken can win a lengthy recount in Minnesota to become their 60th, allowing them to overcome any Republican filibuster. Thune said Republicans hoped to "serve as a counter" to Obama administration proposals on taxes, spending bills and energy.
"We're on a trajectory that I think is going to take us to places that will put us back in a position where we can have more influence," Thune said.
Thune captured attention in 2004 when he defeated then-Senate Democratic Leader Tom Daschle of South Dakota. He is seeking re-election in 2010 and has been viewed by some Republicans as a potential 2012 presidential aspirant. His campaign committee reported nearly $4.4 million in cash on hand at the end of the March reporting period.
Ensign acknowledged last week that he had an affair with a campaign staffer from December 2007 through August 2008. The Nevada senator recently apologized to his Senate colleagues.
Thune has been a consistent conservative voice in the Senate. His campaign recently created a Web site called SupremeCourtWatchOnline.com monitor the deliberations over Supreme Court nominee Sonia Sotomayor.