Canadian actress Genevieve Sabourin was arrested outside Baldwin's New York City apartment in April, after allegedly previously sending him harassing emails and coming uninvited to his Hamptons home.
Sabourin later claimed that she had a friendship with the 30 Rock star dating back to their work together on the film The Adventures of Pluto Nash.
A lawyer for Sabourin filed paperwork in July for a stalking charge to be dismissed, but a US judge has now formally denied that request.
Sabourin will face trial unless her attorneys and Baldwin reach a settlement before her next court hearing on November 27, reports AFP.
Baldwin initially reacted to Sabourin's arrest in April by insisting that he had no relationship with the accused stalker.
"Isn't it odd when an accused stalker is in handcuffs, being taken away by the cops, yet smiles for the cameras?... My friend's text: The last women to smile with handcuffs on were the Manson girls," he tweeted at the time.