This paper evaluates the performance of checkpointing and replication schemes for the fault tolerant mobile agent system. For the quantitative comparison, we have implemented an experimental system on top of the Mole mobile agent system and also built a simulation system to include various failure cases. Our experiment aims to have the insight into the behavior of agents under two schemes and provide a guideline for the fault tolerant system design. The experimental results show that the checkpointing scheme shows a very stable performance; and for the replication scheme, some controllable system parameter values should be chosen carefully to achieve the desirable performance.