In this ever-progressive digital era, conventional e-learning methods have become inadequate to handle the requirements of upgraded learning processes especially in the higher education. E-learning adopting Cloud computing is able to transform e-learning into a flexible, shareable, content-reusable, and scalable learning methodology. Despite plentiful Cloud e-learning frameworks have been proposed across literature, limited researches have been conducted to study the usability factors predicting continuance intention to use Cloud e-learning applications. In this study, five usability factors namely Computer Self Efficacy (CSE), Enjoyment (E), Perceived Ease of Use (PEU), Perceived Usefulness (PU), and User Perception (UP) have been identified for factor analysis. All the five independent variables were hypothesized to be positively associated to a dependent variable namely Continuance Intention (CI). A survey was conducted on 170 IT students in one of the private universities in Malaysia. The students were given one trimester to experience the usability of Cloud e-Learning application. As an instrument to analyse the usability factors towards continuance intention of the application, a questionnaire consisting thirty questions was formulated and used. The collected data were analysed using SMARTPLS 3.0. The results obtained from this study observed that computer self-efficacy and enjoyment as intrinsic motivations significantly predict continuance intention, while perceived ease of use, perceived usefulness and user perception were insignificant. This outcome implies that computer self-efficacy and enjoyment significantly affect the willingness of students to continue using Cloud e-learning application in their studies. The discussions and implications of this study are vital for researchers and practitioners of educational technologies in higher education.