The aim of this study was to evaluate the effect of periodontal treatment on the salivary cytokine levels and clinical parameters of individuals with cerebral palsy (CP) with gingivitis. A non-randomized, clinical trial was conducted in individuals diagnosed with spastic CP. Thirty-eight individuals were enrolled in the study and were categorized according to gingival index scores between 0-1 or 2-3, assigned to groups G2 or G1, respectively. Periodontal treatment comprised oral hygiene instructions, conventional mechanical treatment and 0.12% chlorhexidine applied as an adjunct. Clinical parameters and saliva samples were collected at baseline and at the 15-day follow-up visit. Bleeding on probing and periodontal screening and recording were determined. Non-stimulated saliva samples were obtained, and the salivary flow rate, the osmolality and the levels of cytokines IL-1β, IL-6, IL-8, IL-10, TNF-α and IL-12p70 were evaluated by a cytometric bead array. The Wilcoxon test, the Mann-Whitney test, Spearman correlation analysis, Poisson regression analysis and an adjusted analysis were performed (α = 0.05). The groups differed significantly in periodontal clinical parameters at baseline and at follow-up. Salivary flow rate and osmolality were similar in both groups at both timepoints. However, TNF-α and IL-1β levels were higher in G1 than in G2 at baseline. Mechanical treatment resulted in improved clinical parameters for both groups. Furthermore, mechanical treatment resulted in a significant reduction in salivary IL-1β and IL-8 levels for both groups after treatment. Periodontal treatment performed in individuals with CP and gingivitis reduces the levels of TNF-α, IL-1β, IL-6 and IL-8.