Objectives: To evaluate the clinical, immunological and microbiological efficacy of local application of Thymoquinone (TQ) gel in subjects with grade C periodontitis. Materials and Methods: Twenty-six individuals of both sexes aged between 24 and 37 years, diagnosed as grade C periodontitis with pocket depth ≥5 mm were selected for this study. The patients received a complete prophylaxis including scaling and root planning (SRP) followed by local intrapocket administration of placebo gel in the control group and 0.2% TQ gel in the study group sites. Probing pocket depth (PPD), relative attachment level (RAL), matrix metallo-proteniease-8 (MMP8) concentration in gingival crevicular fluid (GCF) and Aggregatibacter actinomycetecomitans (A.a) count in subgingival plaque were measured and recorded at baseline and 8 weeks postoperatively.