The aim of the present systematic review was to evaluate the efficacy of antimicrobial photodynamic therapy (aPDT) that is used as an adjunctive therapy with scaling and root planing (SRP) in deep periodontal pockets (≥5 mm). The addressed Patients, Intervention, Comparators, Outcomes, and Study design question was: In patients with advanced periodontitis (population), what is the effect of aPDT as adjunct to SRP (intervention) in comparison to SRP alone (comparison) on deep probing depths (outcome)? Electronic and manual literature searches were conducted using the following databases: MEDLINE, Embase, Cochrane Central Register of Controlled Trials, and Cochrane Oral Health Group Trials Register, up to and including February 2018. Six randomized trials were included. All studies used the combined approach aPDT+SRP and SRP in the test and control groups, respectively. The follow-up period ranged from 12 to 48 weeks. Wavelengths, power density, and duration of irradiation used were 670 nm, 500 mW cm , and 60 seconds, respectively. All studies showed significant reduction of probing depth (PD) ≥5 mm with aPDT at follow up. Considering the effects of adjunctive aPDT compared to SRP, only two studies showed additional benefit of adjunctive aPDT in reducing PD ≥5 mm compared to SRP alone at follow up. The overall mean difference for PD reduction (weighted mean difference = 0.31, 95% confidence interval [CI] = -0.03 to -0.66, P = .08) was also not significant between the aPDT and SRP groups at follow up. Whether aPDT as an adjunct to SRP is efficacious in the reduction of PD ≥5 mm compared to SRP alone in periodontal disease remains debatable, given that the available scientific evidence is weak.