Introduction Febrile neutropenia (FN) is a dreaded complication of cancer chemotherapy and frequently associated with respiratory infections. Flexible bronchoscopy (FB) serves as a useful diagnostic tool in this regard. Objective To determine the diagnostic yield, safety and clinical implications of bronchoalveolar lavage (BAL) in cancer patients with FN, having lung infiltrates on radiographic chest imaging. Methods We reviewed medical records of FN patients who underwent FB at Shaukat Khanum Memorial Cancer Hospital and Research Centre, Lahore, from July 2015 till July 2018. The culture yield of BAL, resultant change of management and outcome over the subsequent 30 days were retrospectively analysed. Statistical Package for Social Sciences (SPSS) version 20 (IBM Corp., Armonk, NY) was used for data analysis. Results Ninety FN patients, with mean age 26 ± 18 years and predominantly males (65.6%, n = 59) were included in the study. Seventy-seven (85.6%) had hematological and 13 (14.4%) solid organ malignancy. The mean absolute neutrophil count was 0.20 +/-0.36/ µL. BAL cultures were diagnostic in 40 (44%) patients; the etiology was bacterial, fungal and mixed in 25 (62.5%), 14 (35%) and one (2.5%) patient, respectively. All patients were on empirical antibiotics prior to bronchoscopy: 32 (35.6%) on antibacterial alone and 58 (64.4%) on antibacterial plus antifungal therapy. Change of management occurred in 51 (56.7%) patients after BAL results, including de-escalation from dual antibiotics in 28 (55%) and initiation of new culture sensitive antibiotic in 23 (45%). FB-associated complications developed in three (5.6%) non-intensive care patients (ICU), including transient hypoxia in two and minor hemoptysis in one patient, while five (14.8%) mechanically ventilated patients in ICU experienced worsening of oxygenation parameters within 48 hours. Overall, 24 (26.7%) patients died. Mortality was 3.7% in non-ICU and 69% in ICU setting and significantly higher in patients with fungal pneumonias (p-value 0.01) and with prolonged neutropenia (p-value 0.001).