The three unidentified people entered the Sunshine Public School near the international border in R.S. Pura area of Jammu district around midnight and escaped with the bus.
"They beat up the school guard and tied him up before escaping with a school minibus," a senior police officer told IANS.
"We have traced the minibus which has been recovered in a damaged condition. A manhunt has been launched to trace the three people involved."
State intelligence officials have said the incident is likely the result of some local rivalry and not connected with militancy.