Transcranial alternating current stimulation (tACS) is a non-invasive brain stimulation used for improving cognitive functions via delivering weak electrical stimulation with a certain frequency. This systematic review and meta-analysis investigated the effects of tACS protocols on cognitive functions in healthy young adults. We identified 56 qualified studies that compared cognitive functions between tACS and sham control groups, as indicated by cognitive performances and cognition-related reaction time. Moderator variable analyses specified effect size according to (a) timing of tACS, (b) frequency band of simulation, (c) targeted brain region, and (b) cognitive domain, respectively. Random-effects model meta-analysis revealed small positive effects of tACS protocols on cognitive performances. The moderator variable analyses found significant effects for online-tACS with theta frequency band, online-tACS with gamma frequency band, and offline-tACS with theta frequency band. Moreover, cognitive performances were improved in online- and offline-tACS with theta frequency band on either prefrontal and posterior parietal cortical regions, and further both online- and offline-tACS with theta frequency band enhanced executive function. Online-tACS with gamma frequency band on posterior parietal cortex was effective for improving cognitive performances, and the cognitive improvements appeared in executive function and perceptual-motor function. These findings suggested that tACS protocols with specific timing and frequency band may effectively improve cognitive performances.