The College Prayer Group is managed by the Jesus Youth Team, a missionary movement, by thePrayer young, that is at the service of the Church. It had its beginning in the College in 2009 with a small prayer meeting in the College Chapel. Gradually this prayer meeting grew with more and more young people attending regularly. In the same year, the Jesus Youth prayer group started daily Adoration for an hour from Monday to Friday in the college and that continues till date.

The prayer group reaches out to other colleges, schools, hostels and villages to conduct prayer groups in these places. Other programmes like Leadership Training Programmes, Night Vigils, Village Outreaches and Retreats are also animated by the team. The team in Shillong functions under a Service Team of nine members with a Co-ordinator and an Assistant Co-ordinator and Dr. Fr. Joby Joseph S.D.B, the Rector of St. Anthony's College as the Pastor. Under the Service Team each prayer meeting has its own Core Team that takes care of the members and its activities.

In the College, Jesus Youth prayer meeting is held every Saturday at 3.00 p.m. The Eucharistic Adoration is held on every day of the week from 3.00 to 4.00 p.m. The Team of St. Anthony's College has a Co-ordinator and other team members.