New-onset atrial fibrillation (AF) is frequently observed following acute stroke. The aim of this study was to investigate the effects of the brain-stellate ganglion-atrium network on AF vulnerability in a canine model with acute middle cerebral artery occlusion (MCAO). Twenty-six dogs were randomly divided into the sham-operated group (n = 6), acute stroke (AS) group (n = 7), stellate ganglion ablation (SGA) group (n = 6) and clodronate liposome (CL) group (n = 7). In the sham-operated group, dogs received craniotomy without MCAO. Cerebral ischemic model was established in AS dogs by right MCAO. Right MCAO along with SGA and CL injection into the atrium was performed in SGA and CL dogs, respectively. After 3 days, atrial electrophysiology, neural activity, and the phenotype and function of macrophages in the atrium were studied in all the dogs. Higher AF inducibility (24.4 ± 4.4% versus 4.4 ± 2.2%, P < 0.05) and AF duration (15.7 ± 3.8 s versus 2.6 ± 1.1 s, P < 0.05) were observed in the AS group compared with the sham-operated group, and were associated with increased left stellate ganglion activity, higher macrophage infiltration and higher levels of inflammatory cytokines in the atrium. SGA or CL injection sharply suppressed AF inducibility (5.5 ± 2.7% versus 24.4 ± 4.4%; 5.3 ± 3.2% versus 24.4 ± 4.4%, both P < 0.05) and AF duration (2.9 ± 1.2 s versus 15.7 ± 3.8 s; 3.6 ± 1.0 s versus 15.7 ± 3.8 s, both P < 0.05) in canines with acute stroke. A brain-stellate ganglion-atrium network may increase AF vulnerability through macrophage activation after acute stroke.