The girl, a resident of Naval Pada hamlet in Vikramgadh town, complained of severe pain in abdomen on Wednesday night following which her family admitted her to a local public health care centre, Vikramgadh assistant police inspector R B Mhamunkar said.
It was only after the girl experienced pain and confided in her grandmother about her condition that the family came to know that she had been raped by the relative.
As her condition deteriorated, the girl was rushed to Wada rural hospital, but she died on way near Pali village in the wee hours yesterday.
Based on the complaint, Vikramgadh police have registered an offence under section 376 (rape) of the IPC and relevant sections of Protection of Children from Sexual Offences Act, 2012.
No arrest has been made so far in this connection, police said, adding that they are likely to apprehend the accused today.
The body has been sent for postmortem and further investigation was on.