Brief measures are crucial to assess and identify emotional distress in youth. However, although the assessment of emotional distress in Japan has been demonstrated through measures such as the Japanese version of the negative affect subscale of the Positive and Negative Affect Scale for Children, there remains a need for a brief, stand-alone, screening measure of emotional distress in community and school settings. The purpose of this study was to examine the reliability and validity among Japanese children of the Brief Emotional Distress Scale for Youth (BEDSY), a measure based on anxiety and depression symptoms that load strongly upon the general construct of emotional distress. A total of 5976 children in elementary school or junior high school (grades 3 to 9) completed the Japanese translation of the BEDSY and a short version of the Depression Self-Rating Scale for Children (DSRS-C). Exploratory structural equation modeling for the BEDSY supported a bi-factor model, with anxiety and depression scores loading on a general emotional distress factor, similarly to the original Australian sample. The BEDSY total score correlated significantly and moderately with the Short DSRS-C. Item response theory analyses indicated that each item of the BEDSY was reliable and informative. Differential item functioning supported measurement invariance of the BEDSY between genders and age groups. These results supported the factorial validity, convergent validity, reliability, and potential utility of the Japanese translation of the BEDSY for identifying Japanese youth experiencing emotional distress.