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Septic arthritis and Lyme arthritis are two conditions that can present with similar symptoms, making it challenging to differentiate between them in a clinical setting. While septic arthritis often requires immediate surgical intervention, Lyme arthritis can often be managed effectively with antibiotic therapy alone. However, given the dangerous nature of untreated septic arthritis, accurate diagnosis and timely intervention is crucial in managing the condition, especially in the pediatric population. Efforts to distinguish between the two conditions include the use of laboratory tests, history & physical exam findings, and MRI imaging. The authors aim to explore the causes, presentation, and treatment of septic versus Lyme arthritis, as well as to provide a summary of the evolving research in this area and propose an algorithm that can aid in diagnosis. By synthesizing the proposed algorithm in diagnosis, clinicians will be better equipped to manage septic versus Lyme arthritis effectively while avoiding invasive procedures such as joint aspiration.