In two seasons, he has made two appearances in the NFC title game. Now, he's headed to the Super Bowl, while Dallas Cowboys coach Jason Garrett is traveling to the Senior Bowl looking for prospects.
Sad, ain't it?
San Francisco is 24-7-1 with a pair of NFC West titles, while Dallas is 16-16 without a playoff appearance the past two seasons. Jerry Jones must look at San Francisco's success under Harbaugh and shake his head.
After all, the 49ers hadn't made the playoffs in any of the nine seasons before Harbaugh arrived. They had gone 46-82 and finished as high as second place just twice since 2003.
Only once had they won as many as eight games.
Harbaugh has changed all that. He has written a new narrative. In the process, he has fulfilled his destiny as a football messiah.
Harbaugh has changed the culture and produced wins.
The truth is Harbaugh is everything Jerry hoped Garrett would be the day he hired the Princeton grad, who had never, ever been a head coach. Harbaugh had been a successful head coach at the University of San Diego and Stanford before taking over the 49ers.
He made his dumb mistakes and questionable decisions a long time ago. Garrett's errors get displayed on the professional sports' biggest stage.
Garrett's process to build a winner with staying power works. It's the same process Nick Saban has used to make Alabama and LSU winners.
The problems is Garrett is a process-oriented coach working for a results-oriented owner and he hasn't won enough games to quench Jerry's thirst for success.
No, every organization isn't results-oriented. Sure, every coach must eventually win or he get fired. Still, organizations such as the Pittsburgh Steelers, New York Giants and Tennessee Titans will give a coach an opportunity to work through an average or poor season.
Maybe even two or three of them as long as they believe the coach has the team headed in the right direction.
It's an admirable quality for an organization, and it has served the Steelers and Giants well over the years. They have combined to win four Super Bowls since 2004.
Jerry has just one playoff win since 1997, and if he doesn't get an opportunity to double that total in 2013 then Garrett will get fired.
It's the only choice left.
Jerry's considering firing Garrett as the playcaller and replacing him with offensive line coach Bill Callahan or someone outside of the building.
Doing so will complete a thorough neutering of the head coach that began in the owner's mind the night Washington ended Dallas' season with a 28-18 victory.
Jerry has been on record for more than a decade saying he wants his head coach to call the plays on offense or defense because it gives the players tangible evidence the coach is helping them win games.
Jimmy Johnson didn't call the plays and those Cowboys worked out just fine. Some guys can handle the responsibility and some can't. Clearly, Garrett struggles with it.
Jerry has fired coordinator Rob Ryan and replaced him with 72-year-old Monte Kiffin, who's hiring his defensive staff. Given Jerry's comments since the end of the season, who knows just how much Garrett had to do with those decisions.
But we all know how reluctant Garrett has been to let someone else call plays, so if Jerry takes it from Garrett everyone -- players, fans and media -- will know the coach has been demoted.
So if the Cowboys have success next year, Garrett won't be getting any credit for it.
It will either go to Kiffin for fixing the defense. Or the new playcaller for improving the offense. Heck, Jerry might even get some credit for making the changes after the Cowboys' season ended with yet another thud.
Garrett? He's only going to get credited for staying out of the way. See the situation Jerry has created?
You wonder if a coach -- even one as good as Harbaugh -- could thrive in such a dysfunctional organization.
Garrett has one more season to prove it. Or someone else will get an opportunity to be neutered by Jerry.