Now that he has officially left for the San Francisco 49ers, it will be up to his successor to keep the Cardinal there.
The task will be made much easier because of the talent Harbaugh brought to Stanford, most notably Heisman Trophy runner-up Andrew Luck.
Luck announced Thursday he would stay in school for another year until he graduates rather then become the likely No. 1 pick in the 2011 draft. That surely tempers the blow that hit Stanford a day later when Harbaugh decided to leave for the NFL.
Athletic director Bob Bowlsby will likely want to act quickly to hire a replacement with national signing day less than four weeks away. There are a couple of potential contenders on the Cardinal staff, including offensive coordinator and former Stanford receiver David Shaw and associate head coach Greg Roman.
Bowlsby also could look outside for candidates for a job that figures to be coveted because of Luck's decision to stay in school. Boise State's Chris Petersen might be someone of interest who Stanford looks to interview.
"I trust that Bob Bowlsby will do the right thing," Harbaugh said. "There's no question there are tremendous coaches on the Stanford staff. I respect his process. He may or may not ask my opinion. I've said on record and am well documented in saying that any of the nine coaches that were on our staff I would work for. I think that much of all of them."
Luck was the runner-up this season to Auburn's Cam Newton for the Heisman Trophy and will now be one of the favorites for next year's award.
Luck capped this season by completing 18 of 23 passes for 287 yards and four touchdowns in the fifth-ranked Cardinal's 40-12 victory over No. 12 Virginia Tech in the Orange Bowl on Monday night.
That helped Stanford (12-1) extend its school record for wins in a season and has the Cardinal poised to finish in the top five of the AP poll for the first time since the unbeaten 1940 team finished No. 2.
"We are grateful to Jim Harbaugh for re-energizing the Stanford football program over the past four years," Stanford president John Hennessy said. "He helped build momentum that we are confident will continue into the future. We made Jim the best offer we could commensurate with our role as a university. We wish him the best of luck and look forward to his continuing contributions to football in the Bay Area."
Harbaugh engineered quite a turnaround from the 1-11 team he took over from the fired Walt Harris in December 2006. Harbaugh immediately made his impact on campus by challenging USC coach Pete Carroll.
Harbaugh backed that up with a memorable upset of the Trojans in his first year. He also led the Cardinal to a win over rival California. He fell one win shy of a bowl bid his second year before finally breaking through last season.
Led by 2009 Heisman Trophy runner-up Toby Gerhart and Luck, the Cardinal had their best season in years. They beat Oregon and USC in consecutive weeks to move into the AP poll for the first time since 2001, stayed in contention for a Pac-10 title until late in the season, and earned their first bowl bid in eight years. Stanford lost the Sun Bowl to Oklahoma when Luck sat out with a broken right index finger.
The Cardinal followed that up with perhaps their best season ever this year.
"Coach Harbaugh has led the program with integrity, vision, enthusiasm and energy and his teams have played with precision and exceptional passion," Bowlsby said. "Jim has been a relentless recruiter and he has been successful in enticing some of the finest scholar-athletes in the nation to attend Stanford University. We wish Jim all the best with his new challenges and we know that he will continue to be highly successful."