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Past studies showed that indigenous students are underrepresented in higher education and they tend to have lower academic performance and are more atrisk of dropping out compared to non-indigenous students. Because of the scarcity of local studies, the specific challenges faced by indigenous students during postsecondary education in the Malaysian context are unclear. Indigenous students may encounter various psychological and non-psychological challenges. They are regarded as having significantly lower adaptation and are more prone to psychological problems, such as low self-esteem, compared to the nonindigenous students. These challenges often lead to lower academic achievement, which eventually resulted in withdrawal from the higher education institution. Hence we need to explore the challenges and psychological issues faced by indigenous students during postsecondary education in Malaysia. This study aims at filling in the literature gap by conducting a study on indigenous students at three selected Malaysian public universities. Because the research problem is a fairly unchartered area, a mixed method sequential explanatory study was employed for a better understanding of the research problem. Twelve indigenous students and 2 administrators were chosen for the in-depth semistructured interviews. Thematic analysis was employed to analyze qualitative data. To further understand these challenges according to students’ demographic profile, 51 indigenous students were chosen to respond to questionnaires. The instruments used are the Adaptation Scale by Baker and Siryk (1989) and Self-Esteem Scale by Heatherton and Polivy (1991). The quantitative data were analyzed using SPSS version 21.0. Findings showed that social and academic adaptation and self-esteem were issues among the indigenous students. In addition, transitions into university and new programs may also pose certain challenges to indigenous students as first-year students and those enrolled in pre-diploma programs were found to have lower adaptation and self-esteem compared to their seniors. Low self-esteem seems to be a persistent issue cutting across all demographic profiles.