The aim of this study was to investigate the effects of adjunctive periodontal therapy of 5 mg/mL indocyanine green irradiation by an 810 nm diode laser (aPDT), supplementary to scaling and root planing (SRP) in patients with periodontitis and type II diabetes mellitus (DM) compared to the SRP alone, on periodontal clinical parameters and glycated hemoglobin A1c (HbA1c). The study was conducted on 49 subjects with type II DM and periodontitis, divided into two groups: the SRP group (n = 25), who followed SRP alone, and the SRP + aPDT group (n = 24), who followed SRP and four weekly sessions of indocyanine green irradiation by an 810 nm diode laser. Plaque Index (PI), Bleeding on Probing Index (BOP), probing depth (PD), clinical attachment loss (CAL) and HbA1c were investigated at baseline and after 6 months. At 6 months, both SRP alone and SRP + aPDT generated significant reductions in all the investigated parameters; SRP + aPDT produced more significant reductions for BOP, PD and CAL (p < 0.001) but not for PI and HbA1c, than SRP alone. aPDT with indocyanine green therapy was well tolerated, with two subjects reporting slight discomfort. Therefore, aPDT with indocyanine green might represent a good adjunctive periodontal treatment option for SRP in patients with type II DM and periodontitis.