Migrant students, including refugees and international students who begin or continue their education in Turkey, encounter several challenges. This study aimed to identify the challenges that migrant students face in the Turkish higher education system. The sample of the study consisted of 75 migrant students from six universities in Turkey in the 2019-2020 academic year. Demographic information of the students was gathered utilizing a survey that yielded information on students' gender, age, nationality, length of stay in Turkey, intention to stay in Turkey, ownership of Turkish citizenship, the reason for migration, and future plans. Qualitative data were collected via semi-structured interviews and focus group discussions. Analyses of the data revealed school-related challenges, such as courses and contents, communication, culture, discrimination, exams, homework, physical conditions, registration, and rules. Besides the school-related ones, there were language learning challenges stemming from the Turkish language and English language learning processes.