Empathy is assumed to be a universal human motivation to act altruistically toward others. Developmental models of empathy explaining when and how children acquire the capacity to empathize have been proposed. However, the existing knowledge is largely built upon studies conducted in the Western context. To fill this gap, a cross-culturally validated measure of empathy for children is needed. The purpose of this study was to assess the Japanese version of the Empathy Questionnaire (EmQue), a parent-reported measure of empathy in preschool children, including its construct validity, measurement invariance across genders, and reliability. A total of 550 children aged 1-6 years participated in this study (M[subscript age] = 4.17 years, SD = 1.21). Their mothers completed the Japanese EmQue. Confirmatory factor analysis confirmed the hypothesized three-factor structure (emotional contagion, attention to others' feelings, and prosocial actions) in the 13-item Japanese EmQue. The internal consistencies of the three scales were high. Measurement invariance across gender groups was also supported. Overall, the results demonstrate that the Japanese EmQue is a reliable and valid measure of the empathy of Japanese preschool children. It can serve as a tool in future studies to elucidate the role of culture in shaping empathy in early childhood.