Purpose: Transanal endoscopic microsurgery (TEM) is the most standardized method for the local excision of rectal neoplasms. Unfortunately, local excisions of rectal lesions by means of TEM are not completely free from undesirable functional sequela. This study was performed to evaluate the risk factors of major loss of function after TEM. Methods: Eighty-nine patients underwent TEM between 2019 and 2020. Anorectal manometry was performed before the surgery and 3, 6, and 12 months after the surgery. The quality of life (QoL) was assessed using the Fecal Incontinence Quality of Life scale. Results: The major decrease in QoL was observed in women in 3 months after the surgery in terms of lifestyle and frustration domains (3.6 and 3.64 points, respectively). In 3 months after the surgery, there was a significant decrease in resting pressure both in male and female patients (P=0.01). This difference remained significant 6 months after the surgery (P=0.01). In 12 months after the surgery, resting pressure returned to the preoperative level in most patients (P=0.50). A significant decrease in manometric parameters appeared when the surgery time is more than 55 minutes (P=0.05), the tumor localization is lower than 3 cm from the anus (P=0.03), and the tumor size is over 3 cm (P=0.001). Conclusion The most significant risk factors for the development of functional disorders after TEM are surgery time of >55 minutes, tumor localization at <3 cm from the anal verge, and tumor size of >3 cm.