Stuart Lynn Dunn was arrested in Los Angeles earlier this month after following the 28-year-old "Black Swan" beauty to her gym three days in a row, reported TMZ Online.
Kunis contacted cops on the third day after Dunn allegedly confronted her in the parking lot as she left the building and he was subsequently charged with two counts of felony stalking.
Dunn appeared in court on Friday and protested his innocence, the judge expressed concerns about Dunn's behaviour and set bail at the unusually high figure.
The judge also issued a new protective order against the 27-year-old suspect as part of his bail terms, banning him from going anywhere near Kunis.
Dunn had previously been ordered to stay away from Kunis for three years after breaking into her vacant home in January and inhabiting the property.