Smith was charged Oct. 9 with three felony counts of illegal possession of an assault weapon, stemming from a party at his home in June 2012.
49ers coach Jim Harbaugh said on his weekly radio show with 95.7 The Game that Smith met with 49ers officials Wednesday at team headquarters. General manager Trent Baalke said last week in London that Smith would have to show "progress" to play again this year.
Smith will be due in court twice — Nov. 12 and Nov. 19 — to face DUI and weapons charges.
The 24-year-old Smith had been on what the team called an indefinite leave of absence from the NFC champion Niners. Smith's agent didn't immediately return requests for comment Thursday.
Harbaugh traded text messages with Smith when he was gone, and the coach said on the radio "he's made quite a bit of progress."
While Smith is likely to face a suspension from the NFL, the league typically waits until all legal issues are resolved before handing down its own discipline.
Also in September, Smith and former teammate Delanie Walker were named in a lawsuit filed in Santa Clara County Superior Court by a Northern California man who said he was shot at a party at Smith's house on June 29, 2012.
The players charged a $10 admission and $5 per drink, the lawsuit said. Smith and now-Titans tight end Walker, 29, were allegedly intoxicated on Smith's balcony when they fired gunshots in the air while trying to end the party, the lawsuit said.
Before the 2012 home opener last September, Smith was the passenger in a car during an accident in Santa Clara County in which the driver swerved to avoid hitting a deer. Smith sustained a cut beneath his right eyebrow. He apologized and insisted he would change his ways.
Smith, selected seventh overall in the 2011 draft out of Missouri, had previously been arrested on suspicion of DUI in January 2012 in Miami shortly after the 49ers lost in the NFC championship game.
There was no NFL minimum for the number of games he had to miss while on the non-football injury list. The 49ers continued to pay Smith his weekly salary of more than $98,000 while he was away.
Smith played in a 27-7 home loss to the Colts on Sept. 22 and had five tackles just two days after he was arrested and jailed on suspicion of DUI and marijuana possession. Smith apologized for his behavior after the game then later announced he would leave for treatment.
Smith set a franchise record with 19 1/2 sacks last season.