Abstract Background Carney complex is a rare syndrome characterized by skin pigmentation, endocrine disorders, and myxomas. It is particularly notorious for its tendency to exhibit aggressive cardiac myxomas. Herein, we present a case of a juvenile female patient diagnosed with Carney complex who underwent a right lateral mini-thoracotomy. Case presentation A 13-year-old girl presented with sudden-onset left hemiplegia and dysarthria. Magnetic resonance imaging revealed multiple areas of restricted diffusion. Echocardiography identified a tumor in the left atrium, suspected to be related to Carney complex based on her medical history and physical examination findings. Surgery was performed via right lateral mini-thoracotomy, which minimized the risk of embolism and ensured a cosmetically favorable outcome. The left atrial wall defect was repaired with autologous pericardium. At 3 years postoperatively, follow-up echocardiography indicated no tumor recurrence and normal cardiac function. Conclusions Ongoing follow-ups are essential due to the aggressive nature of the Carney complex and its high recurrence rates. Right lateral mini-thoracotomy offers the advantage of avoiding re-sternotomy and minimizing adhesion dissection, making it the optimal choice for this case.