Background The purpose of this study is to evaluate the effect of a six-week combined manual therapy (MT) and stabilizing exercises (SEs), with a one-month follow-up on neck pain and improving function and posture in patients with forward head and rounded shoulder postures (FHRSP). Methods Sixty women with neck pain and FHRSP were randomized into three groups: Group 1 performed SE and received MT ( n = 20), Group 2 performed SE (n = 20) and Group 3 performed home exercises (n = 20) for six weeks. The follow-up time was one month after the post test. The pain, function, and head and shoulder angles were measured before and after the six-week interventions, and during a one-month follow-up. Results There were significant within-group improvements in pain, function, and head and shoulder posture in groups 1 and 2. There were significant between-group differences in groups 1 and 2 in head posture, pain, and function favoring group 1 with effect size 0.432( p = 0.041), 0.533 ( P = 0.038), and 0.565( P = 0.018) respectively. There were significant between-group differences in both intervention groups versus the control group favoring the intervention groups. Conclusion These findings suggest that both interventions were significantly effective in reducing neck pain and improving function and posture in patients. However, the improvement in function and pain were more effective in Group 1 as compared to Group 2, suggesting that MT can be used as a supplementary method to the stabilizing intervention in the treatment of neck pain. More researches are needed to confirm the result of this study. Trial registration UMIN000030141 modified on 2018.03.08. This study is a randomized control trial registered at UMIN-CTR website, the trial was retrospectively registered and the unique trial number is UMIN000030141 . Electronic supplementary material The online version of this article (10.1186/s12891-019-2438-y) contains supplementary material, which is available to authorized users.