While botulinum toxin injections (BTX-A) have been long used to treat myofascial pain (MFP) in the neck and shoulder region, the evidence of its effectiveness remained unclear. Thus, we aimed to examine the existing evidence on the efficacy of BTX-A injections for reducing MFP in the neck and shoulder areas. This was a systematic review of Medline, Embase, Cinahl, Scopus, and Central databases. Only randomized controlled trials were included. Random effects meta-analysis with effect size index as weighted mean difference (WMD) was applied. The search resulted in 100 records, of them seven were considered relevant and included in the meta-analysis. In total, the data from 261 patients were analyzed. Five trials focused on entire neck/upper back and shoulder pain, one on the infraspinatus muscle and one on the trapezius muscle. The dose of BTX-A varied from 20 to 400 UI. The risk of systematic bias was high for three trials and low for four trials. The pooled WMD was statistically significant [−10.22 (95% confidence interval (CI) −12.77 to −7.68)] on a scale from 0 to 100 in favor of BTX-A over sham. However, the difference was not clinically significant. Also, the meta-regression coefficient was insignificant [−0.01 (95% CI −0.04 to 0.02)]. The overall quality of evidence was moderate. In conclusion, there is moderate evidence that BTX-A injections are not more effective than saline injections to treat MFP in the neck and shoulder region. The effect of BTX-A did not exceed the level of clinical significance. So far, BTX-A cannot be recommended for clinical use when dealing with MFP in the neck and shoulder.