Scedosporium boydii infections pose diagnostic challenges due to their nonspecific clinical manifestations and slow growth characteristics in conventional cultures. This paper highlights the diagnostic value of molecular technology combined with targeted prolonged culture for rare fungi. Unitl now, only one case was identified using metagenomic next-generation sequencing (mNGS). This case represents the first report of a 20-day delayed culture confirmation of S. boydii guided by mNGS results in a non-immunocompromised chronic obstructive -with history of COPD who was admitted with fever and cough. Despite two weeks of antibacterial treatment, chest computed tomography (CT) showed worsening infection. To clarify the pathogen, mNGS and bacterial culture of bronchoalveolar lavage fluid (BALF) were performed. Subsequent culture and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) confirmed the growth of Scedosporium species. Based on clinical presentation, chest CT findings, mNGS results, pulmonary Scedosporiosis was diagnosed, and an antifungal treatment regimen (200 mg BID orally) was initiated. Subsequent culture confirmed S. boydii growth and antifungal susceptibility results were also obtained. After six weeks of voriconazole treatment, he was discharged from the hospital and continued to take oral medication for three months. He was fully recovered without recurrence after six months of follow-up. The present case suggests that mNGS findings can unveil cryptic pathogens like Scedosporium. Use mNGS results to trigger intentional, extended targeted cultivation- challenging standard incubation times- especially in non-immunocompromised hosts with underlying lung disease. Seamless clinician-laboratory collaboration is paramount for treatment success.© 2025. The Author(s).