A 4-year-old boy presented with fever and lymphadenopathy. Despite antibiotic treatment for suspected lymphadenitis, there was minimal improvement. A lymph node biopsy revealed granulomas, raising suspicion of cat scratch disease (CSD). The boy had been scratched by a kitten a month prior. Metagenomic testing of the tissue confirmed the presence of Bartonella henselae, the causative agent of CSD. It is important to incorporate molecular diagnostic tools into clinical practice for precise and timely diagnosis of infectious diseases.