University chancellor Ronnie Green, who did not hire Eichorst, said in a statement that while Eichorst made positive contributions to the school, his "efforts have not translated into on-field performance."
"We're not satisfied with the results," Green said in a news conference with university president Hank Bounds.
The firing is effective immediately, and Nebraska will immediately begin a search for its next athletic director. Eichorst, hired in October 2012 from the University of Miami, will be paid the approximately $1.7 million remaining on his contract, which runs through June 2019.
An interim AD will be named soon. Nebraska plans to use a search firm to assist in the hiring, Green said, and no timetable exists to find a replacement for Eichorst, who took over for Tom Osborne at Nebraska in 2013 and was groomed at Wisconsin by Barry Alvarez. The Badgers' longtime athletic director, Alvarez is a former football player for the Huskers.
"Our fans and our student-athletes deserve leadership that drives the highest levels of competitiveness, as well as excellence across all facets of Husker athletics," Green said in a statement.
The stunning move comes just days after Eichorst, in a rare impromptu meeting with reporters, expressed his frustration and anger over Nebraska's 1-2 start to the season. He reiterated his support for third-year coach Mike Riley, whom he hired to replace Bo Pelini after the 2014 season.
Green and Bounds met with Eichorst earlier Thursday as well as with Riley and the other Nebraska coaches to inform them of the decision.
According to the university leaders, Eichorst's dismissal does not impact Riley, who is 16-13 in his third season at Nebraska after six losses in nine games that followed a 7-0 start last season.
"This is not about Mike Riley right now," Bounds said.
Riley addressed Eichorst's firing after practice Thursday and said he was "taken back" by the decision.
"I was probably flat-out saddened by the whole deal," he said. "I really, really enjoyed working with Shawn. Besides being a good man, I think he had everyone's best interests at heart, coaches and student-athletes. Department-wide, the way it was run, was beautiful. The things put in place to help develop young people were great, and the support we got was at the highest level. His interaction with us was the most I've ever had.''
Riley said he "wasn't going to worry about" the implications of Eichorst's departure.
"We're going to first think of our players and coaching them," Riley said. "We have a great opportunity to do that every day. If your energy goes in a good place, then you can feel good about doing good work. We're just going to continue to do our job and build this team to the highest level daily, so that we can do better on the weekends.
"We need to have better weekends."
Eichorst may still have been fired this week if the Huskers had beaten Northern Illinois, Green said.
"We want to compete," Bounds said, reiterating the theme of his and Green's message. "We're going to figure that out."
Eichorst said in a statement that he was "deeply disappointed" in the decision but "grateful" for his time at Nebraska.
"I am proud of how our student-athletes," Eichorst said. "Coaches and staff represented this great university and state, and I am confident that the future is bright for Nebraska athletics."
Green, hired in April 2016, said the university will reach out to "stakeholders knowledgeable of Nebraska athletics," as well as other athletic administrative leaders around the country, to help in the search.
"Winning can and often does happen in concert with well-run, quality college programs that work to ensure the success of the student," Green said in a news release. "That's our expectation. We take pride here in doing things right and doing the right thing, and that won't change. This is not an either-or equation. We can and should win in that kind of environment."
Eichorst fired Pelini despite a 67-27 record at Nebraska, saying at the time that the Huskers "weren't good enough in the games that mattered." But many attributed the move to a personality clash between Eichorst, who did not hire Pelini, and the polarizing coach, who criticized Eichorst and called him vulgar names during a final meeting with Huskers players.
Former Nebraska quarterback Tommy Armstrong said Thursday via Twitter that he and his teammates felt disrespected by Eichorst at the time of Pelini's firing and that Eichorst failed to properly explain why the move was made.
I'll say what most of us previous players wanted to say. From day 1 he didn't give us a good first impression def during that first meeting
— Tommy Armstrong Jr. (@Tommy_Gun4) September 21, 2017
When he fired Bo as a athlete you would want your boss to tell you before walking into a empty building with no clue of what happened.
— Tommy Armstrong Jr. (@Tommy_Gun4) September 21, 2017
Former cornerback Josh Mitchell also tweeted about the firing, writing that he felt the Eichorst never supported the team.
Eichorst hired Riley from Oregon State, noting that his track record on the field and his personality fit well with the culture at Nebraska. However, Riley hasn't matched the level of on-field success Nebraska enjoyed under Pelini.
Earlier this year, Riley's contract was extended through 2020, and Bounds told the Omaha World-Herald last week that the school expected to tack on another year in December.
Eichorst drew criticism last week when the Big Ten announced future schedules that did not include Nebraska's traditional regular-season finale on Black Friday. Following pressure from fans and the media, Eichorst issued a statement saying that he would do whatever he could to ensure Nebraska's Black Friday tradition would continue.
Nebraska hosts Rutgers on Saturday to open Big Ten play.
ESPN's Adam Rittenberg contributed to this report.