Background Invasive fungal infections (IFI) mainly caused by aspergillus species are one of the leading causes of death in patients undergoing immunosuppressive therapy for hematological malignancies. The presence of galactomannan in bronchoalveolar lavage fluid (BAL GM) is an important diagnostic marker. Some of the factors affecting the BAL GM are still unknown. Antifungal treatment administered before or after BAL also affect BAL GM results. Methods To investigate the effect of BAL GM timing on the diagnosis of IFE, 100 patients receiving immunosuppressive therapy with hematological malignancy at the Uludağ University Faculty of Medicine, Hematology Department, and underwent BAL over a 3-year period with the suspicion of IFE as well as 127 BAL procedures of these patients were examined. Results There were 70 patients who started antifungal therapy before BAL and 30 patients who did not. BAL GM was found positive in 33 (47.1%) of the 70 patients who received antifungal therapy compared to 22 (73.3%) of the 30 patients who did not receive antifungal therapy. There was a significant difference between the two groups in terms of BAL GM positivity (p = 0.016). Subsequently, 127 BAL procedures of these 100 patients were evaluated. When the second, third, and subsequent BAL procedures of the same patients were included in the study, BAL GM was positive in 41 (46.6%) of the 88 procedures in patients who received treatment before BAL and in 25 (64.1%) of the 39 procedures in patients who did not receive treatment before BAL. The rate of BAL GM positivity did not differ between groups (p = 0.068). Conclusions The balance between reducing the risk by initiating early antifungal therapy and maximizing the diagnostic value of BAL GM should be evaluated individually for each patient.