After graduation from high school in Palo Alto in 1982, Harbaugh returned to Ann Arbor and enrolled at the University of Michigan and played quarterback for the Wolverines, starting for three seasons.

In 1995 with Indianapolis, he led the Colts to the AFC Championship Game, was selected to the Pro Bowl and was honored as NFL Comeback Player of the Year.

"[11] As a freshman in 1982 Harbaugh, age 18, and junior Dave Hall were backups to quarterback Steve Smith who had broken Michigan's single season record with 2,335 yards of total offense in 1981.

[13][14] Even as Smith struggled, coach Schembechler expressed a reluctance to play Harbaugh, saying, "To suddenly pull some freshman out of the bag, I don't think you can do that in today's football.

On October 6, 1984, a 19–7 loss to Michigan State in the fifth game of the season, Harbaugh sustained a badly broken left arm in the third quarter when he dove for a loose ball and collided with Spartan linebacker Thomas Tyree.

[30] Harbaugh was the starting quarterback in all 12 games for the 1985 Michigan Wolverines football team that compiled a 10–1–1 record, outscored opponents 342–98, defeated Nebraska in the 1986 Fiesta Bowl, and finished the season ranked No.

In the fourth quarter, Harbaugh completed a 77-yard touchdown pass to wide receiver John Kolesar, giving Michigan a 10-point lead with nine minutes remaining.

"[35] Columnist Mitch Albom wrote after the game that Harbaugh's pass to Kolesar was an image that would last: "The image that repeats will be that of Jim Harbaugh dropping back in the fourth quarter and uncorking a soaring spiral that rose high and long as flanker John Kolesar ran underneath it, his steps seemingly in sync with the revolutions of the ball, so [that] when it fell, it fell right into his arms, almost gently.

[78][79] In 1995, Harbaugh achieved career highs in completion percentage (63.7%), passer rating (100.7), and touchdown passes (17) and led Indianapolis to the AFC Championship Game.

[84] On December 31, 1995, in the AFC Wild Card Round against San Diego, Harbaugh scored on a 3-yard quarterback sneak in the fourth quarter after a 32-yard interception return by Jason Belser and Indianapolis won 35–20.

[87] Aaron Bailey dropped Harbaugh's last-second Hail Mary pass in the endzone, and the Pittsburgh Steelers won 20–16 and went on to Super Bowl XXX, which they lost to the Dallas Cowboys.

[94] Defending AFC Champion Pittsburgh Steelers defeated Indianapolis in the Wild Card Round 42–14 as Harbaugh completed only 37.5% of his passes (12 of 32) for 134 yards, one touchdown, and one interception.

[104][105] Baltimore won its next game 24–10 over the New York Jets on September 13; Harbaugh started and made 5 of 10 passes for 36 yards but again left early and was replaced by Zeier due to injury.

[106] Coach Marchibroda again split quarterbacking duties in the following game on September 20, a 24–10 loss to the Jacksonville Jaguars, with Harbaugh starting and Zeier taking over during the second quarter.

[118] In his debut with San Diego in the September 19 season opener (Week 2), Harbaugh threw two touchdowns in 15-for-27 passing for 159 yards in a 34–7 win over the Cincinnati Bengals.

[124][125] Harbaugh returned in Week 7 (October 24) in a 31–3 loss to the Green Bay Packers as backup to starter Erik Kramer; both quarterbacks threw 3 interceptions each.

With 17 seconds left, Chris Penn caught Harbaugh's attempt at a game-winning touchdown pass albeit slightly outside the back of the end zone.

[140] In the final play of the game, following a 47-yard kickoff return by Ronney Jenkins, Marquez Pope intercepted Harbaugh's attempt at a 50-yard Hail Mary pass that was intended for Trevor Gaylor in the end zone.

[190] On January 7, 2011, four days after winning the Orange Bowl, Harbaugh agreed to a five-year, $25 million contract to become the head coach for the San Francisco 49ers.

Smith was ranked third in the NFL in passer rating (104.1), led the league in completion percentage (70%), and had been 19–5–1 as a starter under Harbaugh, while Kaepernick was considered more dynamic with his scrambling ability and arm strength.

[209][210] Smith was medically cleared to play the day before the next game, but Harbaugh chose not to rush him back and again started Kaepernick, who threw and ran for a touchdown in a 31–21 win over the New Orleans Saints.

[219] In the 2013 season, Harbaugh led the 49ers to a 12–4 regular-season record and a third consecutive appearance in both the playoffs and NFC Championship, where they lost to the Seattle Seahawks 23–17, who went on to win Super Bowl XLVIII.

[227] York claims Harbaugh and the 49ers agreed to mutually part ways immediately after a win over the Arizona Cardinals in the final week of the regular season.

In a game that went to two overtime periods, Ohio State defeated the Wolverines 30–27; Harbaugh said afterward he was "bitterly disappointed with the officiating", especially for a controversial 4th-and-1 call, and was reprimanded by the Big Ten with a $10,000 fine.

Following the loss, according to Harbaugh, the Big Ten acknowledged that there were errors made by the officials on multiple calls, including one that could have resulted in a Michigan touchdown.

Michigan advanced to the Big Ten Championship Game for the first time, where the Wolverines defeated Iowa in Indianapolis, 42–3, earning an Orange Bowl berth against Georgia in the College Football Playoff.

[305] The Wolverines improved to 11–0 by defeating Illinois on a last-minute field goal, 19–17, then won a second straight Big Ten East Division title with a 45–23 victory over Ohio State.

[316] On November 10, the Big Ten Conference announced another three-game suspension against Harbaugh, as part of the investigation into the Michigan Wolverines football sign-stealing scandal.

Although Jim I know, and he's been on the right side of this issue for quite some time.In the aftermath of the murder of George Floyd by an on-duty police officer, Harbaugh expressed his outrage and said, "All injustice should be confronted and punished.

Gattis credited Harbaugh for "the fairness and promotion of black coaches in leadership roles like David Shaw, Derek Mason, Willie Taggart, Jim Caldwell, Pep Hamilton" and himself.