Police have cordoned off the Burnett St house where the body was found.
Dunedin Clutha Waitaki Relieving Area Commander Inspector Jason Guthrie said the woman appeared to be in her early 40s.
The death is being treated as unexplained, and police are not seeking anyone else.
Police said it appeared the body had been there for some time.
No further details will be released until a formal identification has been completed and all next-of-kin have been notified.