Soy foods have had an important dietary role in Asian countries for centuries, and in recent years they have become increasingly popular in Western countries as a result of their suggested health benefits. Nevertheless, there are some concerns that soy can have a negative effect on thyroid function and can alter the levels of thyroid hormones. The aim of this systematic review was to investigate the link between soy or soy product consumption and thyroid function via the measurement of thyroid hormone levels. A systematic review and meta-analysis was undertaken on all randomised controlled trials of studies including soy as an intervention and where free triiodothyronine (fT3), free thyroxine (fT4) and thyroid stimulating hormone (TSH) was measured. The search included PubMed, MEDLINE, EMBASE, Cochrane and sources for the grey literature. Quantitative data synthesis was performed using a random-effects model, with standardized mean difference (SMD) and 95% confidence interval as summary statistics. A total of 18 articles were suitable for review. The meta-analysis showed no significant changes in fT3 (WMD: 0.027 pmol/L, 95% CI: -0.052, 0.107, p = 0.499; I2: 55.58%), fT4 (WMD: -0.003 pmol/L, 95% CI: -0.018, 0.011, p = 0.656; I2: 87.58%) while an elevation in TSH levels was observed (WMD: 0.248 mIU/L, 95% CI: 0.001, 0.494, p = 0.049; I2: 80.31%) levels with soy supplementation. There was no evidence of publication bias. Soy supplementation has no effect on the thyroid hormones and only very modestly raises TSH levels, the clinical significance, if any, of the rise in TSH is unclear.