Background and Objective: There is a strong relationship between trigger points with neck pain and headache. This study aimed to compare the effects of muscle energy technique using low-level laser on reducing neck and shoulder pain and disability in patients with myofascial trigger points in the upper trapezius and levator scapula muscles. Materials and Methods: This double-blinded randomized controlled trial was performed in Zahedan in 2009. Thirty patients with trigger points in the upper trapezius and levator scapula were randomly assigned to one of the three groups in equal numbers. In the laser group, a low-level Ga-As laser was applied with a pulse duration of 200 ns and 6 J/cm2 dosages. By contrast, in the muscle energy group, we used stretching following post-isometric relaxation, and in the placebo group used low-level laser without an output. A 10-session treatment program was performed for each group. Prior to and following the intervention, We assessed the cervical ranges of motion with a goniometer, and neck and shoulder pain and disability with Neck Disability Index and Shoulder Pain and Disability Index respectively. Paired t-test and one-way Anova were used for data analysis. Results: The data shows that the neck pain decreased from 8.2 ± 1.2 to 3.5 ± 0.85 in the muscle energy group, and from 8.4 ± 1.4 to 2.6 ± 1.2 in the laser group. The shoulder pain and disability decreased from 102.9 ± 10.7 to 24 ± 10.3 in the muscle energy group, and from 104.7± 11.8 to 22.6 ± 10.7 in the laser group (P<0.05). There were no significant differences seen between the two treatment groups regarding either the neck and shoulder pain or disability or ranges of motion (P>0.05). Conclusion: The results show that low-level laser and muscle energy technique are both equally effective in decreasing the neck and shoulder pain and disability in patients with myofascial trigger points in trapezius and levator scapula muscles.