Coronary artery calcium (CAC) scoring CT is a useful tool for screening coronary artery disease and for cardiovascular risk stratification. However, its efficacy in patients with coronary stents, who had pre-existing coronary artery disease, remains uncertain. Historically, CAC CT scans of these patients have been manually excluded from the CAC scoring process, even though most of the CAC scoring process is now fully automated. Therefore, we hypothesized that automating the filtering of patients with coronary stents using artificial intelligence could streamline the entire CAC workflow, eliminating the need for manual intervention. Consequently, we aimed to develop and evaluate a deep learning-based coronary stent filtering algorithm (StentFilter) in CAC scoring CT scans using a multicenter CAC dataset. We developed StentFilter comprising two main processes: stent identification and false-positive reduction. Development utilized 108 non-enhanced echocardiography-gated CAC scans (including 74 with manually labeled stents), and for false positive reduction, 2063 CAC scans with significant coronary calcium (average Agatston score: 523.8) but no stents were utilized. StentFilter’s performance was evaluated on two independent internal test sets (Asan cohort- and 2; n = 355 and 396; one without coronary stents) and two external test sets from different institutions (n = 105 and 62), each with manually labeled stents. We calculated the per-patient sensitivity, specificity, and false-positive rate of StentFilter. StentFilter demonstrated a high overall per-patient sensitivity of 98.8% (511/517 cases with stents) and a false-positive rate of 0.022 (20/918). Notably, the false-positive ratio was significantly lower in the dataset containing stents (Asan cohort-1; 0.008 [3/355]) compared with the dataset without stents (Asan cohort-2; 0.043 [17/396], p = 0.008). All false-positive identifications were attributed to dense coronary calcifications, with no false positives identified in extracoronary locations. The automated StentFilter accurately distinguished coronary stents from pre-existing coronary calcifications. This approach holds potential as a filter within a fully automated CAC scoring workflow, streamlining the process efficiently.