The victim was kidnapped from Nalasopara in Palghar on Saturday night last week.
Her body was found in a ladies' toilet at Navsari railway station in south Gujarat on Sunday evening, the Government Railway Police (GRP) official said.
The police suspect that the girl was killed after being kidnapped, he said.
He said after the postmortem at the Navsari civil hospital, the body was yesterday handed over to the Palghar police officials who had come along with the father of the deceased to Navsari, which is located around 280 km from Ahmedabad and about 200 km from Nalasopara.
Meanwhile, the Tulinj police in Palghar's Virar division said the girl was kidnapped from outside her house in Nalasopara on March 24 by an unidentified woman.
The girl's father, Santosh Balchandra Saroj, had subsequently approached the police which lodged a case of kidnapping under Indian Penal Code (IPC) section 363.
Deputy Superintendent of Police Jayant Bajbale of Virar division said they have obtained the CCTV footage of the area where the girl lived.
She later took away the girl, who was at that time playing with other children, he said.
The CCTV footage showed the woman walking along with the girl for about 1.5 km, DSP Bajbale said.
"The police suspect that the woman was either a resident of the locality or acquainted with the area. Our probe is heading in that direction," he said.
"On Sunday evening, we got a message that the girl's body was found in Navsari," DSP Bajbale said.
Meanwhile, some angry residents of the area protested outside the Tulinj police station yesterday and demanded immediate arrest of the woman.
The police has now added IPC section 302 (murder) in the case and launched a manhunt for the woman.