The man, who has not yet been identified, entered through an unlocked door of an apartment at 14th Avenue and East Cliff Drive around 5:30 a.m., according to the sheriff's office.
The man went into a bedroom where a woman was asleep, and when the woman awoke, she was startled to find that the man was staring at her, sheriff's officials said.
The woman yelled at the man and ordered him to leave. She called for assistance from her neighbors, which caused the man to flee.
Deputies responded and searched the area but were unable to locate the suspect.
He was described as being a white man, either in his late 30s or early 40s, around 5 feet 10 inches tall with a stocky thick build. He had a full beard and was wearing a black hooded sweatshirt, a black knit cap and black knee-length shorts.
The sheriff's office is advising residents to lock all doors and windows at night and to call 911 if they see a prowler in their home.
Anyone with information about the crime or suspect is asked to call Detective Kelli McCoy at (831) 454-2311, the sheriff office's 24-hour dispatch center at (831) 471-1121 or an anonymous tip line at (831) 454-2847.