Purpose: Clinical significance of reduced vagal activity following pulmonary vein isolation (PVI) for atrial fibrillation (AF) remains unclear. Periesophageal vagal nerve injury following PVI may be a powerful contributing factor of decreased vagal tone. Methods: Drug‐refractory 51 AF patients (31 males, 64 ± 11 years), who underwent successful PVI, were enrolled. We performed esophagogastroduodenoscopy 2 days after PVI and assessed delayed gastric emptying (DGE). Additionally, the coefficient of variance of R-R interval (CVRR) as a surrogate for vagal tone was measured before PVI, as well as at 1 day and 3 months after PVI. The patients were divided into two groups, patients with DGE and patients without DGE, and changes in CVRR were compared. Results: After PVI, 12 out of 51 patients (23.5%) had DGE. The baseline CVRR did not differ between the patients with (n = 12) and those without (n = 39) DGE (median 3.13%, interquartile range 1.69–5.13 vs. median 3.76%, interquartile range 2.96–5.90, P = 0.297). However, CVRR at 1 day after PVI was significantly lower in the patients with DGE than in those without (median 1.49%, interquartile range 0.90–2.19 vs. median 2.59%, interquartile range 1.58–3.86, P = 0.035), and then CVRR at 3 months became similar between the two groups, suggesting that the two groups had different changes in vagal tone after PVI. The recurrence of AF was similar at 3–6 months after PVI between the two groups. Conclusions: A significantly decreased CVRR immediately after PVI is a sign of DGE incidence, implying collateral damage to the esophagus.