Based on a request by social welfare officials of Jharkhand, railway authorities allotted two air-conditioned coaches for travel of the children, police said.
The travel expenses, including rental for the coaches, will be met jointly by Kerala and Jharkhand governments.
Of the total of 153 Jharkhand children brought to the state, 30 have already gone back home with their parents.
A 40-member team of officials of both Jharkhand and Kerala would accompany the children during the journey.
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A total of 10 people have been arrested in connection with the incident since May 24 after 586 children were brought to Palakkad in Kerala by train from states like Jharkhand, Bihar and West Bengal.
The issue has since then snowballed into a major controversy in the state in recent times with some Muslim outfits, including Indian Union Muslim League (IUML),objecting to turning the incident into a ploy to malign orphanages.
The Kerala High Court had on Thursday said there should be a "serious investigation" in the matter.
Taking serious note of the incident, Kerala State Child Rights Protection Commission had directed the state government to take necessary steps to send the children back home.
The children have been kept at state-run juvenile homes of the Child Welfare Society in Palakkad, Malappuram and Thrissur.