The best surgical procedure of patients with secondary hyperparathyroidism (SHPT) has long been controversial. This meta-analysis was the first study to accurately limit the transplantation site to the forearm muscle and compare the efficacy of total parathyroidectomy with forearm muscle autotransplantation (TPTX+AT) versus subtotal parathyroidectomy (SPTX). A literature search was performed using PubMed, Cochrane, and EMBASE databases up to August 2019. The quality of the studies included was assessed using the Newcastle-Ottawa Scale (NOS). Data were analyzed using Stata version 12 (Stata Corp LP, College Station, TX, USA). A total of 11 studies comprising 984 patients were identified. Compared with SPTX, patients in the TPTX+AT group had significantly lower rates of persistent hyperparathyroidism (OR = 6.41; 95% CI 1.01 to 40.8; P = 0.049). No statistically significant difference was observed in symptomatic improvement (OR = 0.384; 95%CI, 0.12–1.27; P = 0.117), radiological changes (OR = 0.95; 95%CI, 0.03–27.82; P = 0.977), recurrence rate (OR = 1.23; 95% CI, 0.70–2.16; P = 0.473), reoperation rate (OR = 1.07; 95%CI, 0.55–2.07; P = 0.848), hypocalcemia rate (OR = 1.48; 95%CI, 0.78–2.78; P = 0.228), postoperative complications (OR = 0.71; 95%CI, 0.24–2.13; P = 0.537), and hypoparathyroidism rate (OR = 0.91; 95% CI; 0.20–4.18; P = 0.902) between SPTX and TPTX+AT groups. Both of the surgical approaches were effective in treating SHPT for chronic kidney disease (CKD) patients. It was suggested that TPTX+AT was superior to SPTX with reference to the rate of persistent hyperparathyroidism, but this conclusion still needed to be tested in large-scale prospective randomized controlled trials. TPTX+AT may be preferred for SHPT patients with convincing reasons to avoid neck reoperation.