Interstitial cells of Cajal (ICCs) play a key role in gastrointestinal smooth muscle contractions, but their relationship with anal canal function in advanced haemorrhoidal disease (HD) remains poorly understood. This study uses deep neural network (DNN) models to estimate ICC presence and quantity in anal canal tissues affected by HD. Haemorrhoidectomy specimens were collected from patients undergoing surgery with the LigaSure device. A YOLOv11-based machine learning model, trained on 376 immunohistochemical images, automated ICC detection using the CD117 marker, achieving a mean average precision (mAP50) of 92%, with a recall of 86% and precision of 88%. The DNN model accurately identified ICCs in whole-slide images, revealing that one-third of grade III HD patients and 60% of grade IV HD patients had a high ICC density. Preoperatively, pain was reported in 35% of grade III HD patients and 41% of grade IV patients, with a significant reduction following surgery. A significant decrease in bleeding ( < 0.0001) was also noted postoperatively. Notably, patients with postoperative bleeding, diagnosed with stage IV HD, had high ICC density in their anorectal tissues ( = 0.0041), suggesting a potential link between ICC density and HD severity. This AI-driven model, alongside clinical data, may enhance outcome prediction and provide insights into HD pathophysiology.