This systematic review and meta-analysis (PROSPERO registration; ref CRD 42020198921) aimed to govern photobiomodulation therapy (PBMT) efficacy in temporomandibular disorder (TMD). PRISMA guidelines and Cochrane Collaboration recommendations were followed. Differences in pain reduction assessment by qualitative measurement with visual analogue scale pain (VAS), pressure threshold (PPT) and maximum mouth opening (MMO) were calculated with 95% confidence intervals and pooled in a random effects model with a subgroup analysis, evaluating the role of follow-up duration. Heterogeneity was analysed using Q and I2 tests. Publication bias was assessed by visual examination of funnel plot symmetry. Qualitative analysis revealed 46% of the 44 included studies showed a high risk of bias. Meta-analysis on 32 out of 44 studies revealed statistically significant intergroup differences (SSID) for VAS (SMD = −0.55; 95% CI = −0.82 to −0.27; Z = 3.90 (p < 0.001)), PPT (SMD = −0.45; 95% CI = −0.89 to 0.00; Z = 1.97 (p = 0.05)) and MMO (SMD = −0.45; 95% CI = −0.89 to 0.00; Z = 1.97 (p = 0.05)), favouring PBMT compared to control treatment strategies. Sensitivity analysis revealed SSID (SMD = −0.53; 95% CI = −0.73 to −0.32; Z = 5.02 (p < 0.0001)) with low heterogeneity (T2 = 0.02; χ2 = 16.03 (p = 0.31); I2 = 13%). Hence, this review, for first time, proposed suggested recommendations for PBMT protocols and methodology for future extensive TMD research.