"Shaun did a heck of a job for us last year despite joining the team in the middle of the season," 49ers general manager Trent Baalke said in a statement Wednesday. "He certainly earned the respect of everyone in our organization for the way he handled himself, both on and off the field, and we are excited to have him back."
Draughn, 28, was signed off the street last season by the Niners after Carlos Hyde suffered a stress fracture in his left foot.
Draughn immediately became the the 49ers' starting running back -- 13 days after he had been released by the Cleveland Browns.
He was a hard-running pleasant surprise, averaging 3.5 yards per carry and rushing for 263 yards in six games -- compared to Hyde's team-leading 470 yards, averaging 4.1 yards per carry in seven games.
But even Draughn was bitten by the injury bug that pestered the Niners last season; he missed the final two games with a knee malady.
ESPN's Adam Schefter and Paul Gutierrez contributed to this report.