This article examines the relationship between Japanese undergraduate students’ English language proficiency and English language-related challenges faced when studying an international business course through English. It also examines English language proficiency thresholds students need to reach in each academic skill (i.e. reading, listening, speaking and writing) to experience a lower level of linguistic challenges. A total of 264 students were surveyed in Tokyo, Japan, and 13 follow-up interviews were conducted. Exploratory and confirmatory factor analyses confirmed the underlying factors in the EMI Challenges Scale loaded onto a priori assumptions of dimensions falling along skill-based constructs. Analysis of questionnaire data revealed that English language proficiency (i.e. TOEIC score) was a statistically significant predictor of challenges in the EMI programme. While no clear discernible threshold was observed, the differences in perceived ease of study at different levels of English proficiency influenced the challenges students reported for each academic skill. Interview data uncovered the multi-faceted nature of how the thresholds are determined not only by language proficiency but also by other factors, such as prior content knowledge, motivation, and the classroom learning environment. Practical implications for pedagogy are also discussed.