Culliver was arrested March 28 after San Jose police say he struck a bicyclist then rammed a witness' vehicle that was blocking him from leaving until officers arrived.
The San Jose Mercury News reports that he entered his plea Friday in Santa Clara County Superior Court.
In 2013, Culliver created controversy by expressing anti-gay sentiments in the lead-up to the Super Bowl. He has since undergone sensitivity training and done outreach work with an organization that supports lesbian, gay, bisexual and transgender youth.
His case is among a string of recent legal problems for 49ers players, including the arrest Sunday of linebacker Aldon Smith.
Culliver is currently set to be a starter. The 49ers, though, are expected to use a high draft pick at cornerback. Still, Culliver is expected to at least be the team's No. 3 cornerback.
The 49ers have interest in extending his contract, which expires after the 2014 season. But this latest issue could cloud matters, as Culliver could face league discipline.
Information from The Associated Press and ESPN.com 49ers reporter Bill Williamson was used in this report.