Background: Bronchoalveolar lavage fluid (BALF) analysis is essential for the accurate diagnosis and management of interstitial lung diseases (ILDs). Despite established guidelines, variability in sample handling may affect diagnostic accuracy. This study aimed to evaluate how different storage conditions impact BALF cell counts and differentials to guide optimal sample handling practices. Methods: Forty patients who underwent BAL at Chiba University Hospital from June to December 2024 were included. BALF samples were allocated into five groups based on processing conditions: immediate analysis within 1 h, storage at either at 4 °C or room temperature (RT) for 6 h, or storage at 4 °C or RT for 24 h. Total cell counts (TCC) and differential counts were measured and compared among conditions. Results: TCC remained stable over 24 h at both 4 °C (p = 0.86) and RT (p = 0.90). Similarly, the percentages of eosinophils, lymphocytes, and macrophages did not significantly change at either temperature (all p > 0.05). Notably, neutrophil percentages showed a significant decline over time under both storage conditions—at 4 °C (p = 0.02) and at room temperature (p < 0.01). Post hoc tests revealed a notable decreasing trend at 6 h and significant reductions by 24 h at 4 °C (p = 0.09 and p = 0.02, respectively), and significant decreases at both 6 and 24 h at RT (p = 0.01, <0.01). Conclusions: Among the various cell types in BALF, neutrophil proportions are particularly susceptible to storage conditions, showing a significant decline over time—especially at room temperature—while other cell types remain stable for up to 24 h. Therefore, prompt processing or appropriate refrigeration of BALF is essential to ensure reliable cytological analysis and accurate clinical interpretation.