The current tally stands at six wins apiece between the two as the pick up back in the AFC West.
Chargers Offensive Coordinator Greg Roman has had a front-row seat to nearly every coaching matchup between the two.
Roman joined Stanford's staff in 2009 before following Harbaugh to the 49ers the next season.
"It's been something," said Roman, who has been around for 11 of the 13 matchups. "Jim was at Stanford, then I came in at Stanford, Pete was at USC down the street and doing a great job there, did an amazing job there, put a dynasty together.
"We came in, and then we get into the NFC West and they were a young, young team. We were kind of ahead of them and all of a sudden those young guys started getting older, they got really good, they had some great teams there," Roman continued.
"Tons of respect for Pete, tons of respect obviously for Jim," Roman added. "Two great coaches and you always know a Pete Carroll coached team, you better be at your best. They're going to bring the best out of you. That's really college, pro, wherever the paths have crossed."
Entering Monday night, Harbaugh has a .689 career win percentage in the NFL. Carroll, meanwhile, is at .587.
Both have helped define this recent era of football, with their teams often leading the pack in terms of success and dominant play style.
And while the two may not send each other a Christmas card each year, both coaches made it clear this week that they have a healthy amount of respect for the other.
"One thing we would certainly see eye to eye on is about competing," Carroll said. "He's always been a great competitor and has battled, even in his playing days and then in his coaching days."
Harbaugh concurred with his longtime rival.
"It's the thing I enjoy the most … the competition," Harbaugh said. "If you ask me, 'Why do I do this? Why do most of us do it?' Speaking for myself, No. 1 on that list is competition. Love to compete.
"You find others who are like that, too, and you have respect for that," Harbaugh added. "Respect for a guy — another player or coach — and it's like looking in the mirror. There's a great mutual respect there."