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Abstract Background "Swiss Cheese" ventricular septal defects represent a serious congenital heart disease with suboptimal clinical outcomes and a lack of consensus regarding its management. This study presents mid-term follow-up results of surgical repairs for "Swiss Cheese" ventricular septal defects, utilizing the two-patch and right ventricle apex-exclusion technique. Methods A retrospective review was conducted on 13 patients who underwent surgical repair utilizing the two-patch and right ventricle apex-exclusion technique at our institution between May 2014 and October 2021. The procedure involved the closure of defects in the outflow tract ventricular septal and the apex trabecular ventricular septal regions using two patches, with concurrent exclusion of the right ventricular apex from the right ventricular inflow tract. Results Median follow-up was 4.9 ± 2.1 years (range: 2–9 years). All cases were successful without mortality or major complications. Two years post-surgery, cardiac magnetic resonance revealed median values for left ventricular ejection fraction, right ventricular ejection fraction, left ventricular end-diastolic volume and right ventricular end-diastolic volume of 63.9% ± 1.8% (range: 61–67%), 49.2% ± 2.6% (range: 46–55%), 39.15 ± 2.11 ml (range: 36.2–42.7 ml), 44.55 ± 3.33 ml (range: 38.7–48.6 ml), respectively. No thrombosis occurred. The latest echocardiography results confirmed normal cardiac function in all cases. Conclusions The surgical repair of "Swiss Cheese" ventricular septal defects utilizing the two-patch and right ventricle apex-exclusion technique is a viable approach with favorable mid-term outcomes. More cases and long-term follow-up results are needed to validate the feasibility and safety of this technique.