The man is said to have unlawfully broken into the woman’s home in the Ticknock area of Cobh at about 2.30am yesterday.
She was on her own at the time and the intruder is alleged to have physically and sexually assaulted her.
Gardaí believe he stayed in the house for a number of hours before taking her car and leaving the area.
The woman alerted the gardaí shortly after he left and they were quickly on the scene.
She was immediately taken to the sexual assault treatment unit at the South Infirmary/Victoria University Hospital where she was medically examined.
She was also treated for unspecified physical injuries.
After she was released from medical care, the woman was interviewed at length by female gardaí and she is said to have provided them with a full statement.
A Garda spokesman said she “was fairly traumatised” by the ordeal.
Gardaí sealed off the house and preserved the scene as they carried out a thorough forensic examination, which was completed after a few hours.
They recovered the woman’s car after a few hours and in the late afternoon confirmed that they “were interviewing a man in connection with the inquiry”.
It is understood the man is in his 50s and comes from the East Cork area.
“The investigation is ongoing and we are following a definite line of inquiry,” said a Garda spokesman.