Atypical lipomatous tumor/well-differentiated liposarcoma (ALT/WDL) is a rare subtype of endobronchial tumor that has been rarely reported in medical literature. Due to its low incidence, distinguishing it from endobronchial lipoma poses a significant diagnostic challenge, necessitating histopathologic and cytogenetic analysis. As of today, the treatment and surveillance protocols for these neoplasms remain poorly defined, often resulting in their misclassification and treatment as endobronchial lipomas. We present a case involving a 72-year-old male who presented with worsening dyspnea and cough. Diagnostic imaging revealed an endobronchial lesion obstructing the left main bronchus. The patient underwent a flexible bronchoscopy that identified a polypoid mass causing significant obstruction, which was subsequently resected via cryoablation. Histopathology confirmed ALT/WDL, supported by genetic analysis revealing chromosomal alterations. Following the intervention, symptoms resolved, with no recurrence on follow-up imaging. Differentiating ALT/WDL from endobronchial lipomas is necessary not only because it influences treatment decisions but also because it can significantly affect the prognosis of patients diagnosed with ALT/WDL. In this case, we emphasize the importance of considering ALT/WDL in the differential diagnosis of endobronchial tumors and highlight the use of flexible bronchoscopy as a viable substitute for rigid bronchoscopy, serving not only as a diagnostic tool but also as a therapeutic method.