Introduction Japan has experienced a shift toward a multicultural society, and an increasing number of immigrant children have enrolled in its educational systems. Unforeseen experiences may affect the mental well-being of these children and undermine their holistic development; however, research is scarce. This article explores parents’ concern on Nepalese children's experiences in Japanese schools. We aim to reveal the issues that may inform healthcare professionals and schools in best supporting immigrant students. Methods Qualitative survey methods were adopted in an online survey tool to access and collect data from 13 Nepalese parents whose children (age 6–18 years) attended the schools (elementary or junior high school) in four prefectures of Japan. Thematic analysis was used to analyze the data. Results The following four themes were identified: (i) interaction and relationship; (ii) feeling different and meals at school; (iii) academic exclusion—lack of assistance/review at home; and (iv) emotional distress, peer exclusion, and bullying. Conclusion Our findings suggest that because of the linguistic and cultural differences, children had difficulty communicating, leading to poor interpersonal relationships. Subjects reported changes in daily living patterns at home and school, and children felt different, shy, and unable to make friends or get involved. There were problems with school meals as well, and parents expressed concern over a lack of academic assistance. Some noteworthy emotional aspects were inability to be happy at school and bullying or exclusion from peers. They did, however, express the impression that Japanese students and teachers are cooperative. Overall, these findings have implications for schoolteachers, nurses, health personnel, parents, and others who promote the mental well-being and holistic development of children. This study provides a basis for mental health educational programs targeting the relationship between migrant and native students to create an inclusive society for all.