Research on ergonomic risk factors for neck pain among Islamic boarding school students remains scarce, despite their prolonged study and Qur’an memorization activities in static sitting postures. Non-neutral body posture during learning may increase the risk of musculoskeletal disorders (MSDs), particularly neck pain, which can impair concentration and quality of life. This analytic cross-sectional study aimed to assess students’ body posture during study and memorization activities and to examine its association with neck pain. A total of 72 boarding and non-boarding students participated. Data were collected using questionnaires and the Rapid Upper Limb Assessment (RULA), and analyzed with chi-square tests and logistic regression to obtain prevalence ratios (PR) and p-values. Neck pain was reported by 63.9% of respondents; 72.2% exhibited poor sitting posture, and 80.6% reported moderate-to-severe stress. Bivariate analysis showed a significant association between stress level and neck pain (p = 0.033; PR = 2.19; 95% CI: 1.25–3.83). In multivariate logistic regression, no variable reached conventional statistical significance; however, students with moderate-to-severe stress had a 3.81-fold higher risk of neck pain (p = 0.057). These findings underscore the need for integrated ergonomic and psychosocial interventions in Islamic boarding school settings to reduce neck pain risk among students.
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