Abstract Plexiform fibromyxoma is a rare mesenchymal tumor identified in recent years and presents as a gastrointestinal submucosal tumor that is typically located in the gastric antrum. We report a case of gastric plexiform fibromyxoma in which the diagnosis was difficult despite repeated tissue sampling. Before visiting our hospital, the patient had been followed up for 3 years without a definitive diagnosis despite serial examinations, including computed tomography, endoscopy, endoscopic ultrasound, and endoscopic ultrasound‐guided fine‐needle aspiration. Endoscopic ultrasound‐guided fine‐needle aspiration was reperformed, and endoscopic submucosal dissection for deep biopsy was conducted for differential diagnosis of the tumor. However, histological analysis with immunostaining of tumor samples obtained using these techniques cannot provide a reliable diagnosis. Finally, the tumor was resected surgically because of its increasing size, and subsequent microscopic analysis revealed a multinodular plexiform growth pattern of spindle‐like cells with myxoid stroma. Immunohistochemically, the tumor cells were positive for smooth muscle actin but negative for c‐kit, CD34, and S100. Based on these findings, the patient was diagnosed with plexiform fibromyxoma. No evidence of residual or recurrent tumors was observed at 24 months postoperatively.