Background Kidney disease progression rates vary among patients. Rapid and accurate prediction of kidney disease outcomes is crucial for disease management. In recent years, various prediction models using Machine Learning (ML) algorithms have been established in nephrology. However, their accuracy have been inconsistent. Therefore, we conducted a systematic review and meta-analysis to investigate the diagnostic accuracy of ML algorithms for kidney disease progression. Methods We searched PubMed, EMBASE, Cochrane Central Register of Controlled Trials, the Chinese Biomedicine Literature Database, Chinese National Knowledge Infrastructure, Wanfang Database, and the VIP Database for diagnostic studies on ML algorithms' accuracy in predicting kidney disease prognosis, from the establishment of these databases until October 2020. Two investigators independently evaluate study quality by QUADAS-2 tool and extracted data from single ML algorithm for data synthesis using the bivariate model and the hierarchical summary receiver operating characteristic (HSROC) model. Results Fifteen studies were left after screening, only 6 studies were eligible for data synthesis. The sample size of these 6 studies was 12,534, and the kidney disease types could be divided into chronic kidney disease (CKD) and Immunoglobulin A Nephropathy, with 5 articles using end-stage renal diseases occurrence as the primary outcome. The main results indicated that the area under curve (AUC) of the HSROC was 0.87 (0.84-0.90) and ML algorithm exhibited a strong specificity, 95% confidence interval and heterogeneity (I-2) of (0.87, 0.84-0.90, [I-2 99.0%]) and a weak sensitivity of (0.68, 0.58-0.77, [I-2 99.7%]) in predicting kidney disease deterioration. And the the results of subgroup analysis indicated that ML algorithm's AUC for predicting CKD prognosis was 0.82 (0.79-0.85), with the pool sensitivity of (0.64, 0.49-0.77, [I-2 99.20%]) and pool specificity of (0.84, 0.74-0.91, [I-2 99.84%]). The ML algorithm's AUC for predicting IgA nephropathy prognosis was 0.78 (0.74-0.81), with the pool sensitivity of (0.74, 0.71-0.77, [I-2 7.10%]) and pool specificity of (0.93, 0.91-0.95, [I-2 83.92%]). Conclusion Taking advantage of big data, ML algorithm-based prediction models have high accuracy in predicting kidney disease progression, we recommend ML algorithms as an auxiliary tool for clinicians to determine proper treatment and disease management strategies.