Harbaugh said that the two "most likely" possibilities are that the 49ers retain Smith at $8.5 million for next season as a backup or trade him. Of course, Harbaugh did not rule out any other possibilities, either, while suggesting it's unlikely the team would release him.
"Alex is an excellent football player," Harbaugh said Friday at the NFL scouting combine. "Alex is playing the best football of his career the last two years. We think we have the best quarterback situation in the National Football League. (I) feel strongly about that.
"That'll be a process that plays out. Alex Smith, continuing to be a 49er. Or if a trade occurs in the next weeks or months. Those are two of the most-likely possibilities."
General manager Trent Baalke said he recently had dinner with Smith and his wife, Liz, to talk about the future. Harbaugh he said he has also spoken with Smith, who let Harbaugh know he wants an opportunity to be a starting quarterback next season.
"We've talked. I would categorize it as 'map out' or anything," Harbaugh said. "We've talked. In our conversations, he wants to play, and you can totally understand it."
Colin Kaepernick took over as the 49ers' starting quarterback last season. Kaepernick is scheduled to make $740,000 in 2013. The 49ers can renegotiate his contract after the upcoming season.
The 49ers signed Smith to a three-year, $24 million contract last offseason to return to the 49ers as the starter. On the surface, retaining Smith would appear to mean the 49ers would not be able to use the franchise tag to secure prospective free agent safety Dashon Goldson for a one-year, $7.45 million contract. Harbaugh said any suggestion that the 49ers' roster would suffer in other areas if Smith remained on the team was "overdramatic."