Smith, 28, was due in court for violating a protective court order, which resulted in his arrest on March 23, TMZ reported.
The attorney for Smith argued, to no avail, on Thursday that Smith had never missed a court date and told the court his client planned to attend. The judge then issued the bench warrant, according to the report.
It was the second arrest of the month for the troubled linebacker, who turned himself in and was held on suspicion of three counts of misdemeanor violation of a protective order.
On March 3, Smith was taken into custody by San Francisco police after turning himself in to authorities.
In that instance, he was booked on misdemeanor charges of willful infliction of corporal injury, assault with force likely to produce great bodily injury, false imprisonment and vandalism of less than $400.
The Raiders released Smith on March 5.
Smith's first arrest of the month resulted from allegations that he assaulted a woman. When police arrived to respond to a 911 call, Smith was gone, leading police to issue an arrest warrant.
Smith's fiancee, Shawna McKnight, told TMZ.com that she was the victim of the alleged assault and added that her parents took Smith to a rehabilitation center at his request.
Smith proposed to McKnight on Valentine's Day.
Smith was a first-round pick of the 49ers in 2011 and a first-team All-Pro in 2012, but he has had numerous off-field incidents.
He has faced weapons charges and has been arrested on DUI charges multiple times.
Smith last played in the NFL in 2015, when he played nine games for the Raiders and registered 3.5 sacks.
In November 2015, the NFL suspended Smith for one year because of his legal troubles and violation of the league's substance abuse policy.
Smith has played in 59 games, including 37 starts, during his five seasons in the NFL. He has 47.5 career sacks, including 19.5 in 2012 when he was named All-Pro.