Purpose COVID-19 pandemic has far-reaching psychosocial implications for chronic health conditions. We aimed to investigate whether COVID-19 associated social isolation affects lifestyle and weight control in women with polycystic ovary syndrome (PCOS). Methods We conducted an online survey involving 232 women with PCOS and 157 healthy controls on weight changes, physical activity, sleep and eating patterns using Three-Factor Eating Questionnaire (TFEQ-18), Pittsburgh Sleep Quality Index (PSQI), and International Physical Activity Questionnaire Short Form (IPAQ-SF). PCOS-related quality of life questionnaire (PCOSQ) was also completed by the patients. Results While 48.5% of all participants gained weight, 13.9% maintained a stable weight, and 37.6% lost weight during the 14-week social isolation. The distribution of weight change was similar between groups (p = 0.44). All participants reported a decrease in physical activity (p < 0.001). While eating behavior showed no significant change in both groups, reduced sleep quality was found only in the PCOS group (p < 0.001). In women with weight gain, increase in BMI values was higher in patients (1.3 +/- 1 kg/m(2)) than controls (1.0 +/- 0.6 kg/m(2); p = 0.01). Among those who gained weight, delta BMI values showed positive correlations with delta sleep induction time (r = 0.25, p = 0.001), delta PSQI (r = 0.24, p = 0.004) and delta TFEQ-18 scores (r = 0.25, p = 0.001). Conclusion Weight changes during social isolation are similar in women with PCOS and healthy women. However, within those who gain weight, increase in BMI is more pronounced in women with PCOS. Weight gain appears to be related to alterations in sleep quality and eating habits rather than reduced physical activity. Level III Evidence obtained from cohort or case-control analytic studies.