Now, he wants a promotion to the Senate -- and Majority Leader Mitch McConnell and his allies want to stop that.
Privately, McConnell has made clear to his confidantes that he wants to bolster the candidacy of Stutzman's chief GOP rival, Rep. Todd Young, and push him over-the-top in the May 3 primary, according to sources familiar with the conversations.
Publicly, McConnell's super PAC has made Indiana the first state of the cycle to begin an aggressive TV ad campaign on Young's behalf. And one of the GOP leader's closest allies, the U.S. Chamber of Commerce, is also spending big bucks on the airwaves to promote Young.
The move marks a new front in the simmering wars between the establishment and the right flank of the party, a battle that has dominated the GOP since the 2010 midterms and is roiling the 2016 presidential contest. But in this case, McConnell and his allies appear to be maneuvering to defeat a candidate whom they view not only as weak in a general election -- but also as a potential troublemaker in the Senate GOP Conference, much like Cruz.
In an interview with CNN, Stutzman pointedly accused McConnell of retaliating against him for his vote against Boehner last year, saying it "would be a lot harder" for him now to back the Kentucky Republican as Senate leader if he wins in November. He had previously signaled he'd back McConnell as leader.
"They don't want me to be the next senator from Indiana," Stutzman said. "I think (McConnell) is making a mistake by going after conservatives and trying to pick the nominee in Indiana because we just don't like that."
Stutzman added: "Todd Young is going to vote 'yes' for Mitch McConnell, and Mitch McConnell knows that I voted against John Boehner. ... Todd Young is a yes-man."
It wasn't always a foregone conclusion that Stutzman would be in the middle of a war with the GOP leadership. Last year, in an effort to professionalize his operation, he hired well-connected GOP operatives in Washington who have deep ties to the leadership. He met privately with McConnell at National Republican Senatorial Committee headquarters last summer and had a "cordial" meeting with the GOP leader, according to Stutzman and a McConnell aide. He later even met with a top official at the Chamber of Commerce, and asked the group for its support.
But GOP leaders were skeptical. Stutzman later parted ways with his hired D.C. operatives, was spurned by McConnell and the Chamber and instead allied himself with anti-establishment forces like the Club for Growth and the Senate Conservatives Fund. And now the Indiana Senate primary has become ground zero for the party's internal war with major repercussions for the GOP's ability to hang onto their narrow 54-46 majority in the chamber.
"I don't think (the divide]) has anything to do with conservative principles. ... but it's more a question of who are you associated with and what are your tactics?" said GOP Sen. Dan Coats, whose retirement is spawning the fight for his seat in the Hoosier State. "I think overall McConnell is looking to disprove the narrative that Republicans aren't capable of getting things done."
Former Indiana Rep. David McIntosh, head of the Club for Growth, said his group planned to spend money on TV soon to promote Stutzman. "He is the establishment choice," McIntosh said of Young. "Marlin is the outsider running in the race."
Young declined to be interviewed. But a spokesman said that Stutzman has taken a variety of positions that directly contradict his small-government rhetoric.
"Stutzman has proven he'll toss conservative principle aside if he thinks it benefits him personally," said Trevor Foughty, Young's campaign manager.
A top McConnell aide, Brian McGuire, confirmed that the GOP leader met with Stutzman last year but declined further comment, referring inquiries about the ads to the groups bankrolling them.
Outside war against Stutzman
Soon after the 2014 midterms, McConnell moved swiftly to solidify his hold on the Senate majority. He enlisted his top confidantes to put together a super PAC focusing exclusively on Senate races. That super PAC, the Senate Leadership Fund, made its first ad reservations of the cycle this week: a $230,000 TV and digital ad buy in Indiana. The ad dubs the 43-year-old Young as a "rock-solid conservative."
The ad comes after the group's affiliated non-profit, One Nation, has spent $374,800 in the state, according to Kantar Media/CMAG, a firm that tracks media buys, with ads promoting Young's views on national security.
Asked why his group had decided to make Indiana the state of its first ads of the cycle, Senate Leadership Fund spokesman Ian Prior argued that Young is best equipped to be senator. "We think Todd Young is a strong conservative whose story needs to be told to Republican voters," Prior said.
The Chamber of Commerce has dropped $452,390 in the state, according to Kantar Media/CMAG, as it moves aggressively to prop up Young.
Rob Engstrom, the political director at the Chamber, said that the group did not take into consideration Stutzman's opposition to Boehner as it put its muscle behind Young. Instead, Engstrom argued that Young's views align with the business community's. And he was sharply critical of Stutzman for "looking me in the eye" and privately seeking his group's endorsement at a meeting last June -- only to bash the group publicly after it backed Young instead.
In the interview, Stutzman pushed back, saying, "I don't think there's anything hypocritical at all by asking the Chamber of Commerce for their endorsement" given that he sought support from people of all stripes.
Still, he added: "Their agenda isn't in the best interest of our country all the time."
A Cruz acolyte?
Stutzman, 39, has moved quickly up the ranks -- starting in 2002 when, at age 26, he was elected as the youngest member of the Indiana statehouse. In 2010, he ran for the U.S. Senate seat and won the endorsement of the anti-establishment Senate Conservatives Fund. But he lost in the primary to Coats by 10 points.
In the House, Stutzman not only was among 25 Republicans to vote against Boehner, but he has taken positions that have at times angered his party's leadership. He voted against a procedural rule in 2015 to take up trade legislation, nearly scuttling the bill. The move infuriated GOP leaders since he ultimately backed the trade bill, a major priority of the GOP leadership.
Stutzman, however, has shown a desire to work with GOP leaders at times. And for that reason, McIntosh of the Club for Growth sees the congressman more in the mold of Nebraska Sen. Ben Sasse rather than a bomb-thrower like Cruz, who has capitalized on his high-profile battles with McConnell and GOP senators during his presidential run.
"Marlin is more in the style of a Ben Sasse that stands up for what he believes in but also works with his colleagues," McIntosh said.
Coats, who is staying neutral in the race, declined to say if he thought Stutzman would act like Cruz if he became a senator.
"I'm going to pass on that," Coats said. "They both have rock solid conservative records."
Asked if he would act like Cruz, Stutzman said: "I've got a record in the House that stood for pro-growth, pro-defense and anti-establishment."
An intraparty war about personality
Just four years ago, the veteran GOP Sen. Richard Lugar was defeated in stunning fashion by a tea party insurgent, Richard Mourdock, in a hotly contested primary contest. Yet Mourdock lost the general election to now-Sen. Joe Donnelly after the GOP candidate said that pregnancies caused by rape are part of God's intentions.
Some Republicans warn that Stutzman could be another version of Mourdock, especially since Democrats have fielded a top-tier candidate, former Rep. Baron Hill. Stutzman and his allies sharply push back at that assertion, saying the three-term congressman is battle-tested and would win in the red state.
To other Republicans, this fight is less about electability and more about personality.
In a sign that that may be the case, the National Republican Senatorial Committee, which is in charge of Senate strategy for the GOP, is staying out of the primary. Mississippi Sen. Roger Wicker, chairman of the NRSC, said that either Young or Stutzman would win the general election.
"We're not involved in the primary," Wicker said. "I think our nominee will win that race."
There hasn't been much public polling in the Indiana Senate race, so it's hardly clear how next month's primary will shake out. And it will be overshadowed and likely influenced by the GOP presidential primary, which is also the same day.
Democrats say thanks to the likelihood that it'll either be Donald Trump or Ted Cruz as the GOP nominee, their party could pull off an upset in the conservative state's Senate race.
"They're all kind of vulnerable -- especially with either Cruz or Trump at the top of the ticket," said Montana Sen. Jon Tester, chairman of the Democratic Senatorial Campaign Committee, when asked about Stutzman versus Young.