The aim of this systematic review was to investigate whether antimicrobial photodynamic therapy (aPDT) as either a primary mode of treatment or an adjunct to non-surgical treatment was more effective than scaling and root planing (SRP) alone in treating chronic periodontitis in terms of clinical attachment level (CAL) gain and probing depth (PD) reduction. The focused question was developed using the Patient, Intervention, Comparison, and Outcome (PICO) format, and two authors independently searched the Medline, EMBASE, Cochrane Library, Web of Science, Google Scholar, and Scopus databases for relevant studies from January 2008 to December 2016. Twenty studies included in this systematic review were randomized clinical trials (RCTs) or quasi-RCTs of aPDT compared to placebo, no intervention, or non-surgical treatment in an adult population. Basic study characteristics, photosensitizing agents and wavelengths used in aPDT, frequency of aPDT application, effect of aPDT on clinical parameters, antimicrobial effect of aPDT in chronic periodontitis, effect of immunological parameters following aPDT and patient-based outcome measures were collected from the studies. Although there was a wide range of heterogeneity in the included studied, they all indicated that aPDT has the potential to be an effective adjunct in the treatment of chronic periodontitis. Long-term, multicenter studies with larger sample sizes are needed before aPDT can be recommended as an effective treatment modality.