The 4-year-old victim, who hailed from Kurla in Mumbai, was on a vacation in Goa at her grandparents place in Quepem.
While the incident happened on Sunday, her body was recovered from an under-construction building in the town yesterday.
According to police, the accused, identified as Dipak Kumar, a labourer, is a married man and hails from Begusarai in Bihar. He has confessed to sexually abusing the girl and killing her on Sunday evening, they said.
The minor victim was playing with other kids, when the accused offered her a chocolate and took her to an under- construction site, where he raped her, police Inspector Santosh Desai said.
Fearing that she would reveal the incident to her grandparents, the accused later killed the girl by strangulating her, Desai said.