Lacrimal gland ductal carcinoma is a rare, highly invasive tumor associated with a poor prognosis, arising from the lacrimal gland ductal epithelium. This study presents a rare case of lacrimal gland ductal carcinoma, analyzed through histopathology, immunohistochemistry (IHC) staining, fluorescence in situ hybridization (FISH), and whole-exome sequencing (WES) following surgical excision. Pathological examination confirmed a lacrimal gland ductal carcinoma with different structure features, including a solid pattern with comedo necrosis, cribriform pattern, and trabecular pattern. IHC assays demonstrated negative expression for P63, Calponin, CK5/6, SMA, S100, CK14, CD117, and GCDFP-15 in the tumor cells, while CK (Pan), EMA, and mammaglobin were positively expressed. Additionally, AR, GATA3, and HER-2 showed focal weak positivity. FISH analysis revealed a positive PLAG1 rearrangement and a negative HMAG1 rearrangement. WES revealed mutations in BAX, RB1, USP48, SDHB, COL17A1, COL6A6, PIK3CG, PIK3C2B, POLE, and APOBEC3G, suggesting these as potential driver genes in lacrimal gland ductal carcinoma. The patient remained alive at the time of this report.