Insufficient physical activity (PA) and excessive sedentary behavior (SB) are detrimental to physical and mental health. This systematic review and meta-analysis aimed to identify whether e-health interventions are effective for improving PA and SB in college students. Five electronic databases, including Medline, Web of Science, Embase, Cochrane Library, and ProQuest, were searched to collect relevant randomized controlled trials up to 22 June 2022. In total, 22 trials (including 31 effects) with 8333 samples were included in this meta-analysis. The results showed that e-health interventions significantly improved PA at post-intervention (SMD = 0.32, 95% CI: 0.19, 0.45, p < 0.001) compared with the control group, especially for total PA (SMD = 0.34, 95% CI: 0.10, 0.58, p = 0.005), moderate to vigorous PA (SMD = 0.17, 95% CI: 0.01, 0.32, p = 0.036), and steps (SMD = 0.75, 95% CI: 0.23, 1.28, p < 0.001. There were no significant effects for both PA at follow-up (SMD = 0.24, 95% CI: - 0.01, 0.49, p = 0.057) and SB (MD = -29.11, 95% CI: -70.55, 12.32, p = 0.17). The findings of subgroup analyses indicated that compared to the control group, interventions in the group of general participants (SMD = 0.45, 95% CI: 0.27, 0.63, p < 0.001), smartphone apps (SMD = 0.46, 95% CI: 0.19, 0.73, p = 0.001), and online (SMD = 0.23, 95% CI: 0.04, 0.43, p < 0.001) can significantly improve PA at post-intervention. Moreover, the intervention effects were significant across all groups of theory, region, instrument, duration, and female ratio. At follow-up, interventions in groups of developing region (SMD = 1.17, 95% CI: 0.73, 1.62, p < 0.001), objective instrument (SMD = 0.83, 95% CI: 0.23, 1.42, p = 0.007), duration <= 3-month (SMD = 1.06, 95% CI: 0.72, 1.39, p < 0.001), and all female (SMD = 0.79, 95% CI: 0.02, 1.56, p = 0.044) can significantly improve PA. The evidence of this meta-analysis shows that e-health interventions can be taken as promising strategies for promoting PA. The maintenance of PA improvement and the effect of interventions in reducing SB remain to be further studied. Educators and health practitioners should focus on creating multiple e-health interventions with individualized components.