A fault tolerant system includes a primary virtual machine that is formed on a primary machine in which a primary hypervisor runs, and is configured to input virtual interrupt based on an external interrupt from the primary hypervisor to a primary guest OS, and a secondary virtual machine that is formed on a secondary machine in which a secondary hypervisor runs, and is configured to input the virtual interrupt to a secondary guest OS on the basis of timing information on the virtual interrupt transmitted from the primary virtual machine. The primary virtual machine is configured to transmit the timing information on the virtual interrupt including the number of branch instructions executed by the primary guest OS before inputting the virtual interrupt, and including an execution suspension position when inputting the virtual interrupt to the secondary virtual machine.