Background: Sacroiliac joint dysfunction frequently contributes to low back pain, causing significant discomfort and functional disability. Aim: This study aimed to evaluate the effect of application of stretching exercise versus stretching exercise and natural method on pain and functional disability among patients with sacroiliac joint dysfunction. Methods: Research design: A comparative, non-randomized quasi-experimental design. Setting and sampling: The study was conducted in the orthopedic department and outpatient clinic at Assiut University Hospitals, involving 290 non-randomized patients divided into two groups: group A (145 patients) received stretching exercises and natural method (massage with warm coconut oil), while group B (145 patients) performed only stretching exercises. Both groups received illustrated brochures and participated in a six-month intervention. Tools: Patients’ assessment form, numeric pain rating scale, Quebec back pain disability scale and Oswestry disability index. Results: Patients’ ages ranged from 20 to 58 years, with a predominance of females (group A: 73.1%; group B: 71.7%). Although both groups showed significant improvements in pain reduction and functional capacity, group A demonstrated statistically more substantial improvement (p < 0.01) in both pain reduction and functional capacity than group B. Conclusion: Incorporating natural method with stretching exercises may provide superior outcomes in managing pain and functional disability in patients with sacroiliac joint dysfunction. Recommendation: It is recommended to integrate natural methods alongside stretching exercises for managing sacroiliac joint dysfunction, as this combination can enhance pain relief and improve functional capacity.