The use of a virtual learning environment is increasingly gaining popularity with universities among students and instructors. VLEs is said to increase flexibility and promote independent learning. However, the pedagogical effects and the contribution of instructors in student's experience of cognitive active learning in these online classrooms is worth investigating. This paper seeks to explore the disparity between students and the instructor's perception of cognitive active learning experience in a VLE. Consequently, this paper utilizes a phenomenological constructivism approach by using interviews and questionnaires as the primary method of data collection. The results show that instructors believe students are often not intrinsically motivated and consequently do not automatically experience deep learning in the VLE without the appropriate instructional support. The instructor must stimulate deep thinking with a well-formed and probing questions or comments which promotes critical thinking and knowledge transference. This highlights the disconnect between the two instructors and learners in the expectations, attitude towards learning, and the learning environment.