A numerical study t predict the characteristics on transient operation of the heat pipe cooling system with multiple heaters for electronic system has been performed. The heat pipe cooling system of 45 cm length and 16 mm diameter was composed of evaporator section with four heaters which simulate electronic components, insulated transport section, and condenser section with a conductor which was cooled under the constant heat flux boundary condition. Two test cases were investigated in present study; Case 1 indicated that the 1st and 2nd heaters among four heaters were heated off, while the 3rd and the 4th heaters were heated on. Case 2 was the inverse situation switched from heating locations of Case 1. Case 3 indicated that the 1st and 4th heaters among four heaters were heated off, while the 2nd and 3rd heaters were heated on. The results showed that the transient time to reach the steady state is shorter for Case 1 than for Case 2. Especially, the maximum temperature among the heaters which simulate electronic components during switching operation is relatively small compared to the maximum allowable operating temperature in electronic system. It is concluded that the heat pipe cooling system in present study operate with the good thermal reliability even for sudden switching situation of the heaters.