The bird, affectionately known as Paula, was spotted by a visitor, and later found lying below its usual perch by Inspector Lee Hopgood, RSPCA officer for Westminster and Camden.
The cause of death has not been established, but foul play is not suspected. Mr Hopgood said; "It definitely looked underweight. There were no visible signs of harm." The body has been taken to London Zoo for a post-mortem examination.
Mr Hopgood had followed Paula's progress over the last 18 months, as sightings were made of a bird of prey in Regent's Park and Camden. It is believed to have escaped from captivity, as eagle owls are not native to Britain.
Paula had been feeding on pigeons nesting around St Paul's and appeared to be in perfect health when sighted last Friday.
Mr Hopgood said: "It's a real shame. I hoped this bird would fare well out of captivity, but obviously not."