Background: Medication non-adherence is a prevalent and complicated problem among patients receiving hemodialysis. Strictly following the prescribed medication regimen is crucial for achieving successful dialysis in end-stage renal disease. Objective: This study aimed to investigate how health literacy and illness perception influence medication adherence in hemodialysis patients. Methods: An observational cross-sectional study was conducted from October 2023 to February 2024 at dialysis units of multisite hospitals across Rawalpindi and Islamabad, Pakistan. A pre-validated, reliable, and interview-based questionnaire was utilized, and a convenience sampling technique was employed to collect data from 390 patients. The Statistical Package for the Social Sciences version 23.0 was utilized for statistical analysis. Results: More than half of the dialysis patients were female, 52.8%, 31% were between the ages of 46–60, and 66.6% had minimal or no education. Of the patients studied, 45.1% exhibited inadequate health literacy, 46.7% held negative perceptions of their illness, and 41.8% demonstrated low levels of medication adherence. The study found a weak correlation: a negative correlation between health literacy and illness perception (r = – 0.080), a positive correlation between health literacy and medication adherence (r = 0.024), and a negative correlation between illness perception and medication adherence (r = –0.061), none of which were statistically significant. Conclusion: A considerable proportion of the patients demonstrate low medication adherence, inadequate health literacy, and negative perceptions of their illness, highlighting the urgent need for targeted interventions. Structured educational programs, motivational interviewing, individual or group support, and in-person or remote (web- or telephone-based) counseling can help address these issues. Additionally, healthcare professionals-led interventions by doctors, pharmacists, and nurses play a crucial role in raising awareness, enhancing medication adherence, and optimizing treatment outcomes.