Objective The risk of atrial fibrillation (AF) and stroke in patients with peripheral artery disease (PAD) is an important issue that has not been investigated adequately. Our aim with the present study was to explore trends in the incidence of AF and stroke in patients with PAD. Methods We employed Danish nationwide registers to identify all patients with first-time diagnosis of PAD (aged ≥18 years) between 1997 and 2015. Age-standardised incidence rates per 1 000 person-years were calculated to estimate trends of AF and stroke. Risk of AF and stroke was estimated by 1 year cumulative incidence. Results A total of 121.241 patients with first-time diagnosis of PAD were identified. The 1-year cumulative incidence of AF in patients with PAD were 1.97% for year 1997-2000, 2.63% for year 2001-2005, 2.66% for year 2006-2010 and 2.78% for year 2011-2015, respectively. The 1-year cumulative incidence of stroke in patients with PAD were 2.71%, 2.71%, 1.95% and 1.81%, for the 1997-2000, 2001-2005, 2006-2010 and 2011-2015 year groups, respectively. Likewise, the age-standardised incidence rates showed increasing trends of AF during the study period, whereas trends of stroke demonstrated a decline. During study, the initiation of cholesterol-lowering agents and clopidogrel increased markedly from 7.0% to 51.3% and 0.1% to 5.9%, whereas use of warfarin slightly dropped from 4.29% to 3.21%. Conclusions The incidence of AF in patients with PAD has significantly increased over time, whereas a marked decline has occurred in the incidence of stroke. This may suggest that the secondary prevention strategies aimed at reducing risk of stroke are broadly effective.