Purpose: The main aim of this systematic review and meta-analysis (MA) was to assess the effectiveness of online behavior modification techniques (e-BMT) in the management of chronic musculoskeletal pain. Methods: We conducted a search of Medline (PubMed), Cumulative Index to Nursing and Allied Health Literature (CINAHL), Web of Science, APA PsychInfo, and Psychological and Behavioral Collections, from inception to the 30 August 2021. The main outcome measures were pain intensity, pain interference, kinesiophobia, pain catastrophizing and self-efficacy. The statistical analysis was conducted using RStudio software. To compare the outcomes reported by the studies, we calculated the standardized mean difference (SMD) over time and the corresponding 95% confidence interval (CI) for the continuous variables. Results: Regarding pain intensity (vs. usual care/waiting list), we found a statistically significant trivial effect size in favor of e-BMT (n = 5337; SMD = −0.17; 95% CI −0.26, −0.09). With regard to pain intensity (vs. in-person BMT) we found a statistically significant small effect size in favor of in-person BMT (n = 486; SMD = 0.21; 95%CI 0.15, 0.27). With respect to pain interference (vs. usual care/waiting list) a statistically significant small effect size of e-BMT was found (n = 1642; SMD = −0.24; 95%CI −0.44, −0.05). Finally, the same results were found in kinesiophobia, catastrophizing, and self-efficacy (vs. usual care/waiting list) where we found a statistically significant small effect size in favor of e-BMT. Conclusions: e-BMT seems to be an effective option for the management of patients with musculoskeletal conditions although it does not appear superior to in-person BMT in terms of improving pain intensity.