Senate Republicans elect John Thune as their new leader, replacing Mitch McConnell

WASHINGTON — Senate Republicans selected Sen. John Thune of South Dakota to be their leader in the next Congress, three sources with knowledge of the vote said, replacing longtime leader Mitch McConnell, who is stepping down after a record 18 years.

Thune, the Senate Republican whip, ran against two other senators: John Cornyn of Texas, a former whip, and Rick Scott of Florida, an underdog candidate who just won a second term.

Thune, first elected to the Senate in 2004, has climbed his way up the leadership ladder, previously serving as chair of the Republican conference and chairing the Commerce Committee before ascending to the position of whip in 2019.

Thune ran for leader on a platform of carrying out President-elect Donald Trump’s agenda, although the two men have not always seen eye to eye: Thune rejected Trump’s false claims that the 2020 election was stolen from him.

“I am extremely honored to have earned the support of my colleagues to lead the Senate in the 119th Congress, and I am beyond proud of the work we have done to secure our majority and the White House,” Thune said in a statement. “This Republican team is united behind President Trump’s agenda, and our work starts today.”

The senators met behind closed doors Wednesday to vote by secret ballot, capping a battle that divided the party and pitted Scott, a candidate backed by vocal MAGA allies of Trump, against two long-serving senators with institutional knowledge and deep relationships in the body.

The first round of balloting ended in votes of 23 for Thune, 15 for Cornyn and 13 for Scott, leading to Scott’s elimination, two sources with direct knowledge of the vote said. The race came down to Thune and Cornyn on the second ballot, and Thune won by a vote of 29 to 24, three sources told NBC News.

Thune will be majority leader for the next two years after Republicans won control of the Senate in last week’s elections. He will replace Sen. Mitch McConnell of Kentucky, who is stepping down after an 18-year tenure that made him the longest-serving leader in Senate history.

“As Congress returns to Washington, we must prepare the Senate to advance [Trump’s] agenda legislatively and ensure that the president-elect can hit the ground running with his appointees confirmed as soon as possible,” Thune wrote in an op-ed for FoxNews.com. “The Senate Republican majority will work with President Trump to ensure the Senate calendar allows us to confirm his nominees and pass our shared agenda as quickly and as efficiently as possible.”

Senate Republicans held a candidate forum Tuesday evening after Congress returned from a lengthy recess to hear from all three candidates. And the secret ballot election began Wednesday morning with incumbent and newly elected senators able to vote. Only a handful of members said how they would vote in advance, with most holding their cards close to the vest.

Thune and Cornyn, both elected during George W. Bush’s presidency, hail from an institutionalist wing of the GOP. Both have long-standing relationships within the conference and can claim to be next in line, with each having served as the No. 2 Republican for six years.

Before the vote, Sen. Kevin Cramer, R-N.D., said he was supporting Thune but admitted there’s “very little” difference between him and Cornyn. “Although Cornyn told me yesterday ... people are saying they’re a mirror image of each other. To which I say, I think John Thune would take offense to that,” Cramer said.

Colleagues viewed Scott, elected in 2018, as a more divisive figure, and he has been a vocal critic of McConnell for years. He aligned himself solidly with the party’s MAGA wing and had secured some endorsements for the job from Trump allies, including right-wing commentator Tucker Carlson, billionaire benefactor Elon Musk and Rep. Marjorie Taylor Greene, R-Ga.

"I think I’m uniquely positioned to really help get the Trump agenda done. ... I’m optimistic I’m going to win. I’m talking about the things that people say they care about, and so we’ll see," Scott told NBC News on Tuesday.

But Trump, notably, didn't weigh in. His ability to anoint his chosen leader was complicated by the secret ballot, which means he won't know which senators voted against his preferred candidate — or be able to politically punish them.

All three candidates ran on promises to carry out Trump’s agenda, a clear point of agreement among them.

Thune and Cornyn also touted their fundraising prowess and donations to help colleagues win elections.

In a letter to fellow Senate Republicans on Tuesday, Cornyn wrote, "In order to Make America Great Again, we must Make the Senate Work Again," and he promised to decentralize power.

"To that end, we will reinvest in a Senate committee process to drive an aggressive legislative agenda that secures our border, reduces federal spending, boosts our economy, unleashes the nation’s energy potential, and reverses bad Biden-Harris policies," Cornyn continued. "Our default position for legislation considered on the floor will be an open amendment process managed by the committee chairs to allow for amendments and increase debate."

As part of the leadership shakeup, Sen. John Barrasso of Wyoming was elected by acclamation to the No. 2 position of majority whip after he ran unopposed. And the No. 3 slot features a battle between Sens. Tom Cotton of Arkansas and Joni Ernst of Iowa.

Asked about Cotton's team exuding confidence that he has the votes, Ernst said she is not so sure.

"Kamala Harris thought she had the votes, too," Ernst said.

This article was originally published on NBCNews.com