The incident came into notice when the two minors, both named Deepak, were found missing at yesterday's routine head count, District Probation Officer Yatindra Kumar said.
The boys, aged 14 and 15, are mentally challenged and were sent to the children's home as they are orphans, Kumar said.
While one belongs to Narhera village in Saharanpur, the other hails from Mulhaira village of Sardhana tehsil of Meerut.
The facility officials and staff are concerned about the minors and a case has also been registered in this connection, police said adding that further investigation is underway.