ABSTRACT Objective Neck pain is a prevalent global health concern often accompanied by musculoskeletal symptoms. This randomized controlled trial attempted to contrast the impacts of non-thrust Maitland mobilization and Autogenic inhibition muscle energy technique on chronic mechanical neck pain associated with cervico-thoracic junction hypo-mobility. Methods Sixty participants (24 males and 36 females, aged 18–45 years) were allocated randomly into three equally sized groups (A, B, C). Group A: Maitland mobilization plus conventional treatment, Group B: Autogenic Muscle energy technique plus conventional treatment, while; Group C solely received conventional treatment. Treatment was administered for four weeks, three times a week. Outcome measures: neck pain (The primary outcome measure) assessed by Visual Analog Scale (VAS), disability evaluated through Neck Disability Index (NDI), active range of motion (AROM), and joint position error (JPE) as an indicator of cervical proprioception. All measures were assessed both at baseline and after four weeks of intervention. Results Results showed significant improvements in VAS, NDI, and increased ROM across all groups post-treatment (p < 0.001). While Groups A and B demonstrated superior outcomes compared to Group C, differences between Groups A and B were not statistically significant (p > 0.05). For VAS and NDI, Cohen-d between Groups A and B was 0.31 and 0.31, and for ROM, Cohen-d was 0.37, 0.16, 0.07, 0.29, 0.36, and 0.53 for flexion, extension, right rotation, left rotation, right bending, and left bending, respectively. Furthermore, all groups experienced a significant decrease in JPE, with Groups A and B showing greater improvement than Group C (p < 0.01). Group B exhibited significantly greater improvement in reducing JPE related to specific motions compared to Group A (p < 0.05). Conclusion Cervico-thoracic junction mobilization and the Autogenic muscle energy technique offer enhanced management for mechanical neck pain by improving pain, function, ROM, and cervical proprioception.