The use of e-cigarettes has been increasing in popularity among people, especially young adults. Assessing young individuals’ perceptions of e-cigarettes can help to identify factors that may influence their decision to use e-cigarettes. To examine prevalence, perceptions, and knowledge of e-cigarettes among university students in Jordan, an observational cross-sectional study using an online self-administered questionnaire was conducted among students from public and private universities between October 2020 and January 2021. A total of 1259 university students completed the questionnaire. Approximately, 11% of participants reported e-cigarettes use. Among users, 26.5% used it for the purpose of smoking cessation, while 22% of them used it out of curiosity, and 20.5% used it as they believed it is less harmful than other tobacco products. Multivariate analysis showed that conventional cigarette smokers were independently associated with a better knowledge about e-cigarettes (OR = 1.496, 95CI% = 1.018–2.197, p-value = 0.040). In addition, medical students showed a significantly better knowledge compared to non-medical students (OR = 1.710, 95CI% = 1.326–2.204, p-value = <0.001). In Jordan, e-cigarettes use is less popular compared to other countries. Nonetheless, educational interventions are needed to correct misconceptions about e-cigarettes among young adults.