Farman Ali was detained a day after police arrested his brother Mohammad Arif following the grisly discovery at their house in a remote district in Punjab province.
The pair had been arrested for eating human corpses in the same village in 2011 and served two years in prison in a case that shocked Pakistan.
Arif has told police that Ali stole the body of the two-day-old child from a graveyard in Darya Khan village, around 300 kilometres (180 miles) south of Islamabad, before they cooked and ate it.
Ameer Abdullah, police chief of Bhakkar district where the village is located, told AFP that Ali was detained on Tuesday and the brothers had been brought to court for a remand hearing.
There is no specific offence of cannibalism in Pakistani law, so Abdullah said they had been charged under anti-terrorism laws and for desecrating a human body.
In the 2011 case police found the body of a 24-year-old woman at the men’s house — minus a leg, which they had eaten.
The suspects will undergo psychiatric tests, Abdullah said.
Police said that the men’s wives and family members had left them some years ago and both were living in the house in isolation.