Introduction Migraine, a chronic neurovascular condition influenced by chronic inflammation, shares cytokines and inflammatory mediators with periodontitis, which can exacerbate migraine intensity. Neopterin, a purine nucleotide influenced by inflammation and free radicals, can serve as a marker for both diseases. Aim: This study aimed to measure serum and salivary neopterin levels in chronic periodontitis and chronic migraine patients to establish an association. Materials And Methods: Sixty-eight subjects were randomly divided into two groups of 34 each: chronic periodontitis (CP) and chronic periodontitis with migraine (CP+CM). Clinical parameters and serum and salivary neopterin levels were measured and compared using an independent samples t-test and Mann-Whitney U test. Data analysis was done using SPSS, with a P-value <0.05 considered statistically significant. Results: The mean values of PPD, CAL, and PI were higher in group 2 (CP+CM) than in group 1 (CP), while BI was higher in group 1 (3.52) compared to group 2 (2.94) with all significant differences. Mean serum and salivary neopterin levels were significantly higher in group 2 (447.1 pg/ml; 445.4 pg/ml) than in group 1 (85.20 pg/ml; 94.5 pg/ml). Neopterin can be considered a biomarker for the interrelationship between chronic migraine and chronic periodontitis.