Neural machine translation (NMT) systems have demonstrated promising results in recent years. However, non-trivial amounts of manual effort are required for tuning network architectures, training configurations, and pre-processing settings such as byte pair encoding (BPE). In this study, we propose an evolution strategy based automatic tuning method for NMT. In particular, we apply the covariance matrix adaptation-evolution strategy (CMA-ES), and investigate a Pareto-based multi-objective CMA-ES to optimize the translation performance and computational time jointly. Experimental results show that the proposed method automatically finds NMT systems that outperform the initial manual setting.