Aims: Post-thyroidectomy hypoparathyroidism remains the most frequent complication of thyroidectomy, largely due to inadvertent parathyroid gland (PG) injury, devascularization, or misidentification. Near-infrared autofluorescence (NIRAF) enables intraoperative identification of PGs, while indocyanine green fluorescence (ICGF) allows real-time assessment of gland perfusion. This meta-analysis aimed to evaluate the efficacy of the combined use of NIRAF and ICGF in thyroidectomy. Methodology: A systematic search of PubMed, Cochrane, Scopus, and ScienceDirect was conducted up to October 2025. Reported outcomes included transient hypoparathyroidism, permanent hypoparathyroidism, and number of identified PGs. Bias was evaluated using Newcastle-Ottawa Scale for cohort studies and Cochrane Risk of Bias Tool for Randomized Trials (RoB 1.0 and 2.0). Meta-analyses were performed using Review Manager (RevMan) version 5.4.1. Results: Four studies encompassing 1,127 patients were included. Meta-analysis demonstrated that combined NIRAF and ICGF significantly reduced the risk of transient hypoparathyroidism (RR 0.72; 95% CI 0.54–0.96; p = 0.02) and permanent hypoparathyroidism (RR 0.56; 95% CI 0.35–0.88; p = 0.01) compared with standard care. Additionally, the number of identified PGs was significantly higher in the intervention group (MD 0.33; 95% CI 0.23–0.43; p < 0.0001). The overall risk of bias across studies was rated as low to moderate. Conclusion: Combined use of NIRAF and ICGF demonstrates a significant improvement in PG identification and reduces both transient and permanent hypoparathyroidism.