Background <p>Neck pain is a prevalent musculoskeletal condition that can impact the academic performance and well-being of college students, particularly those in healthcare programs. While both muscle energy technique (MET) and Pilates have shown promise in treating non-specific neck pain, their comparative effectiveness remains unclear.</p> Aims <p>This study aimed to evaluate and compare the effects of Pilates and MET on pain, disability, and deep neck flexor strength in physiotherapy students with non-specific neck pain.</p> Objectives <p>The objective was to assess the effects of Pilates and MET on pain, disability, and neck flexor strength using the painDETECT Questionnaire and Neck Bournemouth Questionnaire.</p> Methodology <p>A total of 32 physiotherapy students were divided into two groups: Group A (Pilates, <i>n</i> = 16) and Group B (MET, <i>n</i> = 16). The painDETECT Questionnaire, Neck Bournemouth Questionnaire, and pressure biofeedback were used to assess pain, disability, and neck flexor strength. Both groups underwent a 3-week intervention, with three sessions per week.</p> Results <p>Both groups showed significant improvements in pain, disability, and neck flexor strength (<i>p</i> &lt; 0.05). The MET group had a slightly greater reduction in pain (− 13.51%) compared to Pilates (− 11.27%), while the Pilates group showed marginally better improvement in disability (− 48.00% vs. − 46.53%).</p> Conclusion <p>MET and Pilates are both effective in reducing pain, improving disability, and enhancing deep neck flexor strength in students with non-specific neck pain. Both interventions present viable treatment options for managing neck pain in college students.</p>