Serum cardiac troponin I (cTnI) is often elevated in patients with ischemic stroke, and is associated with their prognosis. Since cTnI is also closely related to atrial fibrillation (AF), cTnI may be a sensitive prognostic indicator in patients with AF-related stroke. This study aimed to evaluate the association between serum cTnI and early neurological deterioration (END) in patients with AF-related stroke. We included consecutive AF-related stroke patients between 2013 and 2015. END was defined as an increase ≥ 2 in the total NIHSS score or ≥ 1 in the motor NIHSS score within the first 72 h of admission. A total of 1,133 patients with AF-related stroke were evaluated. In multivariable analysis, cTnI [adjusted odds ratio (aOR) = 1.16, 95% confidence interval (CI) 1.00–1.34; P = 0.047] remained significant after adjusting for confounders. Initial NIHSS score (aOR = 1.03, 95% CI 1.00–1.06; P = 0.043) was also positively associated with END; meanwhile, the use of anticoagulants was negatively associated in both vitamin K antagonists (aOR = 0.35, 95% CI 0.23–0.54; P < 0.001) and new oral anticoagulants (aOR = 0.41, 95% CI 0.19–0.89; P = 0.024). In conclusion, higher serum cTnI was associated with END in patients with AF-related stroke.