The prevalence of overactive bladder (OAB) increases with age and can be associated with other co-morbidities, such as cardiac arrhythmia. Unfortunately, commonly used anticholinergic drugs for OAB can affect the cardiovascular system, leading to tachycardia. However, there are no data, which consider the influence of intradetrusor onabotulinumtoxinA injections on heart function in idiopathic OAB patients. The aim of the present study was to evaluate the influence of intradetrusor onabotulinumtoxinA injections on electrocardiogram (ECG) parameters. Additionally, changes in ECG were analyzed in OAB patients without cardiac arrhythmia. Thirty-one patients with cardiac arrhythmia and 31 participants without irregular heart rate (HR) completed the study. ECG measurements were performed in supine positions 2 h before onabotulinumtoxinA injections, 1 h after treatment, and at 2 weeks of follow-up. At week 6, a phone-call survey was conducted to collect data about adverse events. OnabotulinumtoxinA injections were performed with rigid cystoscopy under local anesthesia. We did not observe any clinically significant changes in the analyzed ECG parameters between consecutive measurements. While a slight increase of HR was observed in patients without cardiac arrhythmia, it remained within normal range. Intravesical onabotulinumtoxinA injections are, hence, safe for female patients with cardiac arrhythmia and do not significantly influence changes in ECG.