Objectives: Several researchers have investigated inflammatory cytokines in gingival crevicular fluid (GCF) from chronic periodontitis with clinical parameters after periodontal treatment. The aim of the present study was to identify the inflammatory cytokines present in GCF associated with periodontal pocket healing after scaling and root planing (SRP). Methods: Twenty patients were enrolled, and clinical examinations including probing pocket depth (PPD) and bleeding on probing (BOP) were performed at the first visit, and before and after SRP. The periodontal epithelial surface area (PESA) and periodontal inflamed surface area (PISA) were also calculated. GCF samples were collected before and after SRP to measure the levels of 40 inflammatory cytokines using antibody array. Correlations between changes in cytokine levels and clinical improvements were assessed by single and multiple regression analyses. Results: PPD, PESA and PISA significantly decreased after SRP, while there were no significant differences in the levels of cytokines before (PreSRP) and one week after SRP (PostSRP). Clinical improvements (ΔPPD, ΔPESA and ΔPISA) were calculated using the formula PreSRP-PostSRP, while changes in the levels of inflammatory cytokines were calculated using three formulas: PreSRP-PostSRP, PostSRP/PreSRP and Log(PostSRP/PreSRP). Log (PostSRP/PreSRP) for interleukin-1β (IL-1β) significantly correlated with ΔPESA (R = −0.512). PostSRP/PreSRP and Log(PostSRP/PreSRP) for intercellular adhesion molecule 1 (ICAM-1) significantly correlated with ΔPISA (R = −0.669, −0.573). Two good fit models were generated by multiple linear regression. Log(PostSRP/PreSRP) for IL-1β significantly affected ΔPESA (R 2 = 0.566). PostSRP/PreSRP for ICAM-1 significantly affected ΔPISA (R 2 = 0.615). were not associated with clinical improvements. However, the present study indicates that lower PostSRP/PreSRP ratios for IL-1β and ICAM-1 in GCF lead to a greater decrease in PESA and PISA, respectively. Periodontal pocket healing might be affected by a decreased ratio of inflammatory cytokines such as IL-1β and ICAM-1 at an early stage after SRP.