This study aimed to develop a linezolid-based hydrogel and evaluate its performance as a locally administered medication for treating stage II grade A periodontitis. A biocompatibility test was performed using the MTT assay, and hemolysis assays were conducted at different concentrations (2%, 4%, 6%, 8%, and 10%). This treatment trial included 40 individuals with stage II grade A periodontitis. They divided the participants into two groups. Scaling and root planing (SRP) was the only treatment given to group A (control), while linezolid gel and SRP were given to group B (test). Plaque index (PI), gingival index (GI), probing pocket depth (PPD), and clinical attachment level (CAL) were among the clinical data that were documented both at baseline and three months later. According to in vitro analysis, the hemolysis ratio was less than 1% at 2% concentration, and the biocompatibility assay showed 98% cell viability after 94 hours. In vivo analysis was performed using a hydrogel based on 2% linezolid. All clinical measures (PI, GI, PPD, and CAL) showed statistically significant differences (P < 0.05) between baseline and three months when compared within groups. In addition, a significant difference favoring group B was observed in all metrics on the inter-group comparison (P < 0.05). As a supplement to SRP, locally applied linezolid gel appears to be beneficial for patients with stage II grade A periodontitis.