Background: Burnout, due to extreme mental and physical fatigue, and emotional exhaustion, leads to decreased nursing quality and turnover. However, not all nurses are observed as burnouts in the same work environment, and resilience and related factors may have effects on the development of burnouts. Therefore, we conducted a cross-sectional study to examine the effects of resilience and related factors on the burnout in clinical nurses, Kagoshima, Japan. Methods: Data for this cross-sectional study involving nurses (n = 98) was collected using the following questionnaire surveys: the Bidimensional Resilience Scale, The Workplace Social Support Scale, and the Japanese version of the Pine's Burnout Scale. Using burnout as a dependent variable, analyses were conducted using one-way analysis of variance and multiple regression analysis after adjusted for related factors. Results: The prevalence of burnouts was 19.6% on the mainland and 36.1% on remote island. Innate resilience, acquired resilience, workplace social support, and burnout showed no significant difference between nurses on the mainland and remote island. In the mainland participants, innate resilience (ß = -0.492, P < 0.001) and acquired resilience (ß = -0.325, P = 0.007) showed a negative association with burnout, and similar associations were observed innate resilience (ß = -0.520, P = 0.004) and acquired resilience (ß = -0.336, P = 0.057) in the remote island participants. For all participants, innate resilience (ß = -0.443, P = 0.001) and workplace social support (ß = -0.204, P = 0.031) showed a negative association with burnout, and turnover intention was positively associated (ß = 0.025, P = 0.021). Conclusion: A negative association between burnout and innate resilience factors was observed in the mainland and remote island. Further evaluation of innate resilience is necessary for burnout prevention in clinical nurses.