Stuart Dunn, 27, was arrested earlier this month when he violated a restraining order by following Kunis to her gym three times. Dunn was previously put on probation in January for unauthorised entry onto Kunis's property.
The LA County District Attorney has now confirmed to TMZ that Dunn has been charged with two counts of felony stalking.
Dunn will face up to four years in jail if he is convicted.
Kunis also recently made headlines for coming to the aid of a worker when he suffered a violent seizure at her home.
She next stars with Mark Wahlberg in Seth MacFarlane's Ted, opening on July 13 in the US and August 1 in the UK.
Watch a trailer for Ted below: