Background: Musculoskeletal health issues are increasingly prevalent among students due to prolonged sitting and incorrect postures. Meanwhile, this remains unassessed in the context of traditional Indian educational centers, like gurukul, where students adopt cross-legged sitting postures with minimal use of furniture. Methods: A cross-sectional study was conducted with learners pursuing undergraduate courses in gurukuls at Uttarakhand, Delhi, and Uttar Pradesh. The study used Nordic musculoskeletal questionnaire for musculoskeletal discomfort (MD), observational methods, and focus group discussions. Results: 51 respondents comprised of 86% male (44) and 14% females (07), with 94% aged under 24. 75% respondents were staying in gurukul ≥ 7 years and 90% sat cross-legged ≥ 8 h a day. 67% respondents reported no MD in any body part, while the most prevalent MD was reported in lower back (16%); wrists/hand (10%); knees (8%); and other parts (< 4%) in the past 12 months. The Fisher’s exact test for association revealed no statistically significant relationship (p = 1) between cross-legged sitting hours and MD. Meanwhile, year-wise reporting of MD revealed an interesting trend of reduction in MD with progression in subsequent years. Conclusion: Gurukul learners appear to have minimal levels of MD considering the extended hours of cross-legged sitting and lack of ergonomic furniture.