Motivation is one of the most critical prerequisites contributing to English as a Foreign Language (EFL) students’ academic success. Nonetheless, the connection between students’ motivation and academic low achievement remains underexplored in Vietnam. This study, therefore, drawing from Deci and Ryan’s Self-determination Theory, endeavored to bridge this gap by exploring factors affecting low-achieving high school EFL students’ motivation in learning English, which in turn shaped their academic outcomes. The study adopted a cross-sectional qualitative case study design and conducted semi-structured interviews with four purposefully selected participants. Qualitative data were analyzed via convergent cross-case thematic analysis. Findings revealed that participants’ motivation in learning English was dramatically affected by external and internal factors. External factors included institution-related, family-related, teacher-related, peer-related, and socioculture-related influences. Internal factors encompassed intrinsic motivation in learning English, personal interests in learning English, and self-regulated learning competence. Critically, external factors were perceived to be more influential on their motivation in learning English than internal factors. Subsequently, some pedagogical implications were introduced to relevant stakeholders to enhance teaching practices and foster English learning motivation among this student population.