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Chlamydia pneumoniae is a significant cause of community-acquired pneumonia, yet its diagnosis remains challenging due to non-specific symptoms and the limitations of traditional methods like serology, which can cause delays. We present the case of a 14-year-old female admitted with cough and right-sided chest pain. Initial laboratory tests were unremarkable, except for a positive C. pneumoniae IgM result. A chest CT scan revealed right upper lobe infiltrates. Despite empirical azithromycin, her improvement was limited. Bronchoscopy was performed, and bronchoalveolar lavage fluid was analyzed by targeted next-generation sequencing (tNGS), which identified C. pneumoniae as the dominant pathogen with a high sequence count (9886), providing strong evidence for the etiology. Targeted macrolide therapy was continued (transitioned to oral doxycycline), leading to marked clinical improvement within 72 h. Longitudinal lab monitoring revealed a self-resolving transaminitis and a rise in Serum Amyloid A post-treatment. This case suggests that tNGS can serve as a valuable adjunctive tool in providing a rapid, culture-independent etiological diagnosis for atypical pneumonias, helping to guide effective therapy in selected patients with complex respiratory infections.