Background The aim of the present study was to evaluate the clinical efficacy of the diode laser as an adjunct to scaling and root planing (SRP) and also determine the biochemical profile by evaluating the gingival crevicular fluid (GCF) levels of interleukin (IL)-17, IL-10, tumor necrosis factor-related weak inducer of apoptosis (TWEAK), and sclerostin. Methods A total of 40 systemically healthy, patients with Stage III periodontitis were included in this randomized controlled study. Participants were randomly divided into two groups as SRP + diode laser (L) (0.80W power, 940 nm wavelength and 0.80J/s energy level) and only SRP group. Recording of periodontal parameters and collecting GCF samples were performed at baseline, first and 3rd months. Biomarker levels in GCF were measured with ELISA Results At baseline, no significant difference was detected between groups in terms of both clinical and biochemical parameters. All biochemical parameters (except for IL-10 in control group), presented a statistically significant difference for 3 months study period in both groups. When laser and control groups were compared, significant differences were not observed, except the lower GCF IL-17 levels (P = 0.025), bleeding on probing (P = 0.028), and clinical attachment level (CAL) (P = 0.0002) values in laser group at third, first, and third months, respectively. Statistically significant correlations were also noted between biochemical parameters and clinical parameters. Conclusions The GCF IL-17, TWEAK, and sclerostin levels may be useful for monitoring response to SRP+L therapy. However, long-term studies on higher populations are needed to evaluate the effectiveness of adjunctive use of diode laser application to SRP.