Background Myofascial release (MFR) and Mulligan Sustained Natural Apophyseal Glides (SNAGs) are manual therapy techniques routinely practiced in the management of non-specific low back pain (NSLBP). As a solo intervention or along with other therapies, both methods have reported positive results for individuals with NSLBP. However, which technique improves NSLBP-related pain, restricted range of motion (ROM) and disability, warrants further research. Objective To study the comparative effects of MFR and SNAGs on pain, disability, functional ability, and lumbar ROM in NSLBP. Method A parallel-group study was conducted at tertiary care hospitals. Sixty-five Sub-acute or chronic NSLBP patients were allocated to receive strengthening exercises along with either MFR (n = 33) or SNAGs (n = 32) for six treatment sessions over one week. An independent assessor evaluated outcome measures such as the Visual Analog Scale (VAS), Patient-Specific Function Scale (PSFS), and ROM at baseline, immediate (after 1st treatment), and short-term (post-sixth day of the intervention). The Modified Oswestry disability index (MODI) was assessed at baseline and short-term. Results Within-group analysis found clinically and statistically significant (p < 0.05) changes for VAS and PSFS at immediate and short-term for both the groups. The lumbar extension also showed improvement immediately and in the short-term. Improvement in Lumbar flexion was seen only in the SNAGs group over the short-term. A statistically significant improvement was seen for MODI in both the groups but was not clinically significant in the MFR group. The analysis observed no statistically significant difference (p < 0.05) between the groups at both the immediate and short-term. Conclusions Pain and restricted function associated with NSLBP can be improved using SNAGs or MFR, along with strengthening exercises. For limited lumbar flexion ROM, Mulligan SNAGs have a better outcome than MFR over the short-term. Hence, both manual therapy techniques can be incorporated along with exercises for immediate and short-term management of sub-acute to chronic NSLBP. Clinical Trial Registration. CTRI/2018/12/016787 (http://ctri.nic.in/Clinicaltrials/).