Globalization and migration have led to a multicultural and diverse global society. With increasing numbers of immigrant children, Japanese schools are experiencing diversity. We aimed to fill the gap in understanding the difficulties experienced by immigrant children in Japanese schools with a particular focus on their social, emotional, interpersonal, and psychological well-being. We conducted a qualitative survey among 15 parents of three nationalities (South Korea, the Philippines, and Vietnam). Parents of children aged between 6 and 18 years, and attending Japanese schools (elementary or junior high school) were recruited. Detailed written data were collected from participants in their preferred language. After several rounds of translation by bilingual experts, thematic analysis took place. The insights of participants led to identification of interrelated themes: Language barriers in communication, self-expression, and keeping pace with learning at school; Friendship, establishing satisfactory interpersonal relationships, social connection, and cultural integration; Bullying, discrimination and psychological/emotional well-being; Teachers' care, support, and parental wishes; and Comparisons, preferences, and feedback. Language and cultural differences significantly impact the ability to communicate, develop relationships, and learn. Children's emotional manifestations of these difficulties signify problems with integration, adaptation, and mental well-being, and include fear, feeling lonely, difficulty with friendships, rejection, bullying, and discrimination. Although the strict rules, competitive exams, and monolingual environment in Japanese schools were noted, most families appreciated teachers' support and care, and Japanese education's focus on teaching life skills and teamwork. The findings inform schools, healthcare professionals and other concerned stakeholders about ways to support immigrant students to develop and flourish.