Mechanical removal of microbial biofilm dental plaque from tooth surfaces is important for treatment of periodontal diseases. However, the effectiveness of conventional scaling and root planing (SRP) is affected by the local conditions and residual bacteria which may affect the healing process. We performed a randomized clinical trial to test our hypothesis that adjunctive antimicrobial photodynamic therapy (aPDT) plus SRP has significant effect compared with SRP alone, which can last for 1 year. The study included 136 sites in 16 patients with previously untreated chronic periodontitis, at least one premolar and one molar in every quadrant (minimum, four teeth/quadrant) and at least one tooth with attachment loss of ≥4 mm in every quadrant. In all patients, two randomly assigned quadrants were treated with SRP and the other two were treated with SRP + aPDT. The clinical parameters of probing pocket depth (PPD), bleeding on probing (BOP), and clinical attachment level (CAL) were evaluated at baseline and after 3, 6, and 12 months. There were no significant differences between the two groups at baseline. PPD and BOP showed significant reduction, and CAL showed significant gain from baseline for all three time points in both groups. In addition, there were significantly greater reduction and gain for SRP + aPDT than for SRP at all three time points. No adverse effects of aPDT were observed. These data demonstrate significant improvement in all evaluated clinical parameters for at least 1 year and suggest that aPDT as an adjunctive therapy to SRP represents a promising therapeutic concept for persistent periodontitis.