Background Rothia dentocariosa is a commensal organism of the oral cavity that rarely becomes pathogenic, typically affecting immunocompromised patients or those with indwelling medical devices. This case describes a Rothia dentocariosa infection in a central venous catheter in an 18 months old girl with Pompe disease, providing an opportunity to discuss the benefits and challenges of conservative management to avoid catheter removal in specific clinical contexts. Case Description A 18 months old girl with Pompe disease complicated by severe hypertrophic cardiomyopathy had been treated weekly with specific enzyme replacement therapy through a central venous catheter (Port-a-Cath) for about a year with nearly complete regression of the cardiomyopathy and no complication. Due to the presence of intermittent fever with high spikes associated with shaking chills during enzyme therapy administration the patient was admitted to our ward of evaluation. Clinical examination and echocardiography revealed no sign of endocarditis. Blood cultures drawn from the catheter revealed the persistent presence of Rothia dentocariosa. Although usually considered a contaminant, the positivity in three consecutive blood cultures . With no other infectious foci present, a catheter-related infection was diagnosed. Managing a long-term catheter infection required a careful assessment of the risks and benefits of catheter removal. Considering the low virulence of the bacterium, the patient’s clinical stability, and the high risks associated with catheter reimplantation, a conservative approach was chosen. The patient was treated with daptomycin (10 mg/kg) and amoxicillin/sulbactam (100 mg/kg) for 15 days, with fever resolution by the third day of therapy. After discontinuing antibiotics, follow-up blood cultures were negative, and no infection recurrence was observed at the one-month follow-up. Conclusion This case highlights the potentially advantageous role of conservative management in Rothia dentocariosa catheter-related infections in pediatric patients with specific clinical needs. Documenting similar cases contributes to the knowledge base supporting an individualized and conservative therapeutic approach, preserving long-term venous access and minimizing complications and healthcare costs.