Cody Butler, 19, is alleged to have told police that his daughter got tired and the temperature dropped outside so he put her in the car and turned on the heater to keep her warm.
The toddler had just spent the day with her father and his girlfriend at a playground in Tahlequah, Oklahoma, US. The National Weather Service said the temperature in Tahlequah was about 10C.
Detective Jeff Haney said an initial investigation showed the child had an extremely high core temperature, Fox News reports.
He said Butler was talking outside the vehicle with his girlfriend after leaving the engine running and the heater on.
He took the child from the car when he noticed her cheeks were purple and tried to rescuscitate her while an ambulance was called.
Police Chief Clay Mahaney said: "This type of tragedy is one of the hardest calls we respond to as law enforcement officers.
"We feel for the family and strongly remind everyone to never leave a young child unattended for any amount of time."
Although police are treating the girl's death as an accident, Butler is still facing charges for child neglect and second-degree manslaughter.