BackgroundShoulder and neck pain are reported as the most common occupational-related health problem and cause of morbidity, absenteeism from work among school teachers worldwide. School teachers represent an occupational group, who are exposed and appears to have prevalent shoulder and/or neck pain due to their daily work tasks and the nature of work. There is a scant epidemiological study regarding shoulder and neck pain among school teachers in Ethiopia. Therefore, this study was set out to assess the prevalence and associated factors of shoulder and/or neck pain among school teachers of Gondar town in North West Ethiopia.MethodAn institutional based cross-sectional study was conducted from December 2016 to January 2017, a structured questionnaire adapted from the Nordic musculoskeletal questionnaire was distributed to 848 primary and secondary school teachers in Gondar town, Northwest Ethiopia. To assess the burden of shoulder and/neck pain, data were collected using a self-administered questionnaire and physical measures like height and weight were also measured during data collection. Independent variables which had significant association were identified using logistic regression model.ResultA total of 754 teachers participated, with a mean age of 42 ± 9.73 years (88.9% response rate). Previous 12 months self-reported prevalence of shoulder and/ neck pain among school teachers was 57.3% with 95%CI (53.4–61.0%). Regular physical exercise (OR = 0.18, 95% CI: 0.08–0.42), teaching experience (OR = 2.85, 95% CI: 1.09–7.42), static head down posture (OR = 2.26, 95% CI: 1.55–3.33), elevated arm over shoulder (OR = 2.71, 95% CI: 1.86–3.95), prolonged sitting (OR = 1.50,95% CI: 1.02–2.23) and hypertension (OR = 2.18, 95% CI: 1.24–3.82) were factors found to be significantly associated with shoulder and/neck pain.Conclusion and recommendationMore than half of the study participants self-reported to have suffered shoulder and neck pain in the previous 12 months. Teaching experience, static head down posture, elevated arm over shoulder, and hypertension are likely to be significantly associated with shoulder and/ neck pain among school teachers in Ethiopia. Engaging in regular physical exercise has a protective effect against the shoulder and/or neck pain. Therefore, school authorities are recommended to provide facilities to enhance physical activity among school teachers and also provide adjustable board and classroom materials.Electronic supplementary materialThe online version of this article (10.1186/s12891-019-2397-3) contains supplementary material, which is available to authorized users.