The increased utilization of computed tomography (CT) has led to a higher detection rate of thyroid incidentalomas. Currently, there are no widely agreed-upon guidelines for managing these incidentalomas. This study aims to investigate the prevalence, follow-up practices, and malignancy rates of thyroid incidentalomas detected by CT. We conducted a comprehensive search of PubMed, Embase, and Cochrane databases to identify relevant studies published before April 12, 2024 (PROSPERO #42024535501). Studies reporting on the prevalence, follow-up, and risk of malignancy (ROM) of thyroid incidentalomas detected by CT were included. Combined outcomes were analyzed using pooled proportion (PP) with a random effects model. The risk of bias was assessed using the Cochrane risk-of-bias tool for randomized trials (RoB2) and the Newcastle-Ottawa Scale (NOS) tool. Subgroup analyses were conducted based on characteristics including size of the incidentaloma, CT area, and age of the study population. Thirty-eight studies involving 195959 patients were included in the prevalence analysis, revealing a prevalence of thyroid incidentalomas on CT of 8.3% (95% confidence interval [CI], 7.4-9.3). The prevalence was higher in neck CT (16.5%, 95% CI, 11.0-22.1) compared to chest CT (6.6%, 95% CI, 5.3-7.9). Multiple incidentalomas were found in 27.0% (95% CI, 12.9-41.1) of patients. Of the nodules, 46.3% (95% CI, 32.3-60.3) were ≥1 cm, and 28.6% (95% CI, 19.9-37.3) were ≥1.5 cm. Thyroid ultrasounds, biopsies, and surgeries were performed in 34.9% (95% CI, 26.1-43.7), 28.4% (95% CI, 19.9-36.9), and 8.2% (95% CI, 2.1-14.4) of cases, respectively. Additionally, twenty-five studies with 6272 patients reported a ROM of 3.9% (95% CI, 3.0-4.9) for thyroid incidentalomas detected on CT. A higher ROM was observed in incidentalomas ≥1 cm (11.7%, 95% CI, 3.9-19.4) and ≥1.5 cm (24.9%, 95% CI, 0-52.7) compared to those <1 cm (0.1%, 95% CI, 0-0.8) and <1.5 cm (0%, 95% CI, 0-0.2). Most thyroid incidentalomas identified on CT are benign. Implementing a collaborative protocol between radiologists and thyroid specialists to manage high-risk thyroid incidentalomas can ensure appropriate follow-up and optimal patient care.