The child, admitted to Himmatnagar Civil Hospital four days ago in critical condition, tested positive for Chandipura virus, prompting intensified surveillance.
Director of Public Health Dr T S Selvavinayagam instructed the officials to conduct information, education and communication activities to avoid panic.
Three cases from the neighbouring states - two from Rajasthan and one from Madhya Pradesh - have also been treated in Gujarat hospitals, Health Minister Rushikesh Patel said.