The agreement was confirmed Thursday by New Mexico State Athletics Director McKinley Boston. Walker will be leaving his head coaching position with the Aggies to be an assistant in Jacksonville, where he will serve as the team's defensive backs coach.
"He is going to resign and accept a position in Jacksonville," Boston said Thursday morning. "It's official."
The Aggies have named offensive coordinator Doug Martin as interim coach, while a national search is expected to follow for a full-time replacement. Martin is expected to be among the candidates to replace Walker.
"(Martin will be) interim coach until a permanent head coach is determined," Boston said. "That process has not been finalized."
Speculation heated up Tuesday night that Walker might be headed out of town, following his fourth year at NMSU. He's been in the running for other jobs during past offseasons at the school - once as a possible candidate for the Seattle Seahawks defensive coordinator position and again for a similar position at the University of Texas.
He interviewed Tuesday with Jacksonville, and shortly thereafter the Internet rumor mill picked up steam. The website footballscoop.com reported that Walker accepted an offer from the Jaguars, as did a handful of regional media outlets.
Still, nothing was confirmed until Wednesday, as Walker and his agent Don Yee were seeking a multi-year agreement from the Jaguars - somewhat of a rarity amongst NFL assistant coaches.
A source with knowledge of the agreement with Jacksonville said Walker could get a slight annual raise by taking the pro job, meaning a multi-year agreement gives him some financial protection.
"That was important to the negotiation," Walker said. "And not just that. We have our whole team back. My son and my daughter (attend NMSU). A lot factored in. I twisted and turned at night making this decision."
Walker's departure was somewhat anticipated following the year, a 1-11 campaign that saw the team take steps backward in its progression after a 2011 season where the Aggies finished with a competitive 4-9 record.
It was Walker's fourth season with the program - always a crucial time for a college football coach. He held a 10-40 career record at the school. With the exception of the 2011 Aggies, the other three years saw NMSU remain largely uncompetitive.
Walker spoke frequently during that time of a program that wasn't adequately supported enough to put wins in the record books, making it unfair to judge his coaching acumen entirely on his win-loss standing.
Following the final game of the 2010 season (a 59-24 home loss to the University of Hawaii) Walker said, "I really believe the more you give, the more you get. And I just really believe we have to study what are you giving? Because I think this can get done. I really do. But, it's going to take a pretty detailed plan with everybody involved for us to get it right."
Walker pointed to his competition - schools such as Utah State, San Jose State and Louisiana Tech - saying football investments were not comparable in terms of assistant coaching salaries, strength and conditioning and recruiting.
"Their university, their athletic department, they made a commitment: 'We're going to have a football program,'" Walker said during an October, 2012 interview as it pertained to Utah State.
"I think it's unfair for any head coach to be judged if he doesn't have what his competitors have. You can. If you want to judge me for not doing more with less, OK. That's fine. That's OK," he added later during the interview. "I would tell any head coach, I think that's something you have to pay attention to. You want to make sure you have the resources and things to be competitive."
Boston said despite the lack of wins, he was happy with how Walker controlled the team, players and locker-room culture over the past four years.
"After lots of thought and internal discussion with his family, he thought the transition to an NFL position was one that was a good decision for him and his family," Boston said. "They thought about it long and hard. He feels good about it and we're happy for him."
For the 52-year-old Walker, NMSU was his first head coaching job, coming to the school in 2009 to replace Hal Mumme. Walker was the 33rd coach in school history.
Walker still has four years remaining on his current contract, which pays him a base salary of $363,000 annually. Walker's original contract, which was amended in 2011, stated there was no buyout following the fourth year of the agreement. Therefore, Walker leaves with no buyouts either way.