Background: The World Health Organization (WHO) has recently endorsed thermal coagulation as an alternative to cryotherapy for cervical precancerous lesions. However, the comparative efficacy and safety of these two treatments lack robust support from large-sample data. This systematic review and meta-analysis aim to evaluate the effectiveness and safety of thermocoagulation compared to cryotherapy in the treatment of cervical precancerous lesions. Methods: A comprehensive search of PubMed, Embase, Cochrane Central Register of Controlled Trials (CENTRAL), International Clinical Trials Registry Platform (ICTRP), and ClinicalTrials.gov was conducted from inception. Additional trials were identified through the reference lists of published reviews. Inclusion criteria encompassed original data studies with colposcopically, biopsied, cytologically, or visually inspected (VIA/VILI) identified patients. Studies were required to have a follow-up duration of at least 6 months, a sample size exceeding 20 patients, a follow-up attendance rate exceeding 50%, and involve cryotherapy or thermocoagulation treatments. Results: Inclusive of all patients, thermocoagulation demonstrated a significantly higher pooled cure proportion compared to cryotherapy (85% vs. 81%, z = 2.245, p = 0.025). However, for VIA-positive patients alone, the difference was not statistically significant (80.0% vs. 79%, z = 1.932, p = 0.053). The incidence of pain was comparable between the two treatment arms, while both exhibited a high incidence of vaginal discharge. Thermocoagulation displayed a lower complication rate for intraoperative pain and postoperative vaginal discharge than cryotherapy, providing a higher level of patient comfort. Conclusions: Thermal coagulation proves to be more effective for patients with cervical precancerous lesions, but the effectiveness of the two regimens is similar if only for VIA-positive patients. In terms of complications, thermocoagulation exhibits a similar rate of intraoperative pain and a lower rate of postoperative vaginal discharge than cryotherapy, enhancing patient comfort.