Polycystic ovary syndrome (PCOS) is one of the most common causes of infertility in women of reproductive age. Insulin resistance is a main pathophysiologic feature in these patients. According to some studies, the intake of probiotic bacteria may improve glucose homoeostasis. The aim of this study was to investigate the effect of synbiotics on metabolic parameters and apelin in PCOS patients. This randomised double-blind placebo-controlled trial was conducted on eighty-eight PCOS women aged 19–37 years old. The participants were randomly assigned to two groups receiving (1) synbiotic supplement (n 44), and (2) placebo (n 44) for 12 weeks. Fasting blood samples were taken at baseline and after 12 weeks. The two groups showed no difference in fasting blood sugar (adjusted mean difference: 0·60; 95 % CI −3·80, 5·00, P=0·727), plasma glucose fasting 2-h (adjusted mean difference 2·09; 95 % CI −9·96, 14·15, P=0·134), HbA1c (adjusted mean difference 0·06; 95 % CI −0·09, 0·22, P=0·959), homoeostatic model assessment-insulin resistance (HOMA-IR) (adjusted mean difference: 0·02; 95 % CI −0·99, 1·03, P=0·837), quantitative insulin sensitivity check index (QUICKI) (adjusted mean difference: −0·02; 95 % CI −0·33, 0·29, P=0·940) and C-reactive protein (CRP) (adjusted mean difference: 0·24; 95 % CI −1·61, 2·08, P=0·141) by the end of the intervention. A significant difference was observed in the mean apelin 36 before and after the intervention between synbiotic and placebo groups (adjusted mean difference: −4·05; 95 % CI −7·15, −0·96, P=0·004). A 12-week synbiotic supplementation has no significant beneficial effects on HOMA-IR and CRP in PCOS patients, whereas the level of apelin 36 significantly decreased.