With the evolution of customer’s needs, innovation becomes a core competency of organizations to success in the intense global competition nowadays. Business process orientation (BPO), as “a state of mind” of the organization, emphasizes to employ a customer-and-process-oriented way to rethink and reengineer business. It is interesting and important to understand the role of process-oriented thinking and working in the innovation-driven economy. To better understand BPO, this study applies McCormack’s definition to consider BPO’s influences on innovation in both employee and organization levels in aspect of three main components. Results from questionnaire survey of Japanese companies show that BPO has positive association with employees’ innovative behavior, and then enhance company’s innovation performance sequentially. Meanwhile, employees’ innovation is a mediator in this link. Therefore, BPO supports innovation, but it cannot guarantee success. Motivating all employees to participate and do innovation is a key for generating innovative solutions for customer through being BPO. This paper contributes to the research by understanding the deeper link between BPO and innovation in Japan which is a highly relevant but understudied context. The findings also recommend companies to motivate employees’ innovative behavior as well as improving BPO to being innovative.