Resection of lung metastases in children with solid tumors is regularly hampered by limited intraoperative detectability and relevant operative trauma of the open surgical access. The aim of this study was to analyze thoracoscopic resection of lung metastases in children following CT-guided labeling with coil wires. We retrospectively analyzed data of children and adolescents undergoing this approach at our institution between 2010 and 2022 with regard to technical aspects as well as surgical and oncological data. Within this period, we performed this procedure on 12 patients wherein we resected 18 lesions (1–5 per patient). The median age of patients was 178 months (51–265). The median duration of coil wire placement was 41 min (30–173) and the median surgery time was 53 min (11–157). No conversions were necessary and no intraoperative complications occurred. Complete microscopic resection (R0) was achieved in all labeled lesions and malignant tumor components were found in 5/12 patients. Our study shows that with a careful patient selection, thoracoscopic resection of lung metastases after coil wire labeling is a safe and reproducible procedure in children. Using this approach, lesions that are expected to have a reduced intraoperative detectability during open surgery become resectable. Patients benefit from the minimally invasive surgical access and reduced operative trauma.