The evidence clearly shows that education greatly impacts people’s well-being. Bangladesh has two main education systems—general and traditional religious schooling. The current study aimed to measure the quality of life of madrasa students and find out the factors influencing it. This was a cross-sectional study on a group of madrasa students in the Mirpur area of Dhaka, Bangladesh. Data were collected using two-stage stratified random sampling between April and May 2022. The final sample size was 373. The health-related quality of life (HRQoL) was calculated using the KIDSCREEN-10 index, and the median split was used to categorize the score into ‘good’ and ‘poor’ categories. A p < 0.05 was considered statistically significant for all statistical tests. Among the participants, most (56%) reported having a good HRQoL. The median age (IQR) of the participants was 10.0 (8.0–12.0) years. Most of the participants were male (91%) and were not orphans (95%). The current study also found that a higher feeling of safety (AOR 3.7; 95% CI 1.3–10.4; p = 0.016) increased the odds of having good HRQoL. However, having a present illness decreased the odds (AOR 0.6; 95% CI 0.4–0.9; p = 0.10) of having a good HRQoL. The key results show that the majority reported a good HRQoL. Promoting students’ physical, mental, and social well-being through health education, anti-bullying initiatives, regular school health screening, and institutional & community involvement can help to improve the overall HRQoL of madrasa students.