Stress susceptibility is highly variable among individuals. For those with high stress susceptibility, they have a high risk of developing mental disorders such as depression upon exposure to social stress. Mice also show depression-like behavior following social stress, and the extent of behavioral changes are variable among individuals even under a uniform genetic background. The precise mechanisms that underlie variability in stress resilience among individuals are poorly understood. To elucidate the mechanisms, we focused on the long-term effects of repeated social defeat stress (SDS) in BALB/c mice. Firstly, we investigated how repeated SDS affects social avoidance. As a result, about half of the defeated mice showed social avoidance whereas the remaining mice did not. Interestingly, during 2 weeks after the stress exposure period, some defeated mice changed their behavioral phenotypes from avoidant to non-avoidant or vice versa. To identify brain regions whose activity during social interaction were different between mice that underwent repeated SDS and naïve mice, or between avoidant mice and non-avoidant mice, we focused on c-Fos, a marker for neuronal excitation. We developed a semi-automated whole-brain c-Fos mapping method. Brain-wide analyses led to the identification of several brain regions that exhibit altered c-Fos signal densities in defeated mice. Furthermore, the c-Fos signal densities in the lateral habenula (LHb) were different between defeated mice that showed social avoidance from immediately after the stress exposure period and those that showed social avoidance only at later periods. These results contribute to understanding neural basis that underlies individual variability in stress resilience.