A 22-year-old man and a 19-year-old woman have been held following the discovery at Packett Street, Fenton.
Staffordshire Police was called to the scene at 10:00 BST. A force spokesperson said post-mortem tests would take place on Wednesday.
Formal identification of the child has yet to take place.
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Scenes of crime officers have been examining the property and an alleyway behind it.
Det Insp Dan Ison said: "Our thoughts are with the little girl's family at this time.
"This is a very distressing incident and we are doing all we can to support those affected."
West Midlands Ambulance Service said crews found a child "who was sadly confirmed deceased".
A spokesman said: "They also treated a woman at the scene before she was transported to Royal Stoke University Hospital."
Two people have been arrested on suspicion of murder after a two-year-old girl was found dead at an address in Stoke-on-Trent.