IQ-domain GTPase-activating protein 1 (IQGAP1) is a multidomain scaffold protein that is involved in cytoskeleton dynamics and tumor metastasis. Although the role of IQGAP1 in various cancers had been reported, the function of IQGAP1 in pterygium has not been studied. In this study, surgically excised pterygium and control conjunctival tissue from cataract patients were analysed by immunohistochemistry, confocal microscopy, and Western blot for IQGAP1 expression, mast cell counts, and microvascular count. Pterygium was clinically divided into mild and severe types according to Tan's classification and Kim's criteria based on translucency and vascularity of the tissue. Greater clinical severity of pterygium was associated with higher expression of IQGAP1 expression. Compared to normal conjunctival tissue, severe pterygium had significantly higher IQGAP1 expression (P = 0.005), which strongly correlated to the number of microvessels (P = 0.003) and mast cells (P = 0.01). Confocal microscopy revealed IQGAP1 colocalization with mast cell and CD31. IQGAP1 expression was higher in the pterygium body compared to the head. In conclusion, the level of IQGAP1 expression was found to be correlated to the clinical severity of pterygium. Mast cells were identified in pterygium and is suspected to be involved in promoting fibrovascular invasion.