The focus of this research is on the process of conducting distance education online, which is undergoing rapid transformation due to the impact of digitalization. The primary objective is to examine how cognitive load arising during online distance learning affects the perceived system usability, and the role of cognitive control and flexibility in this relationship. By revealing the direct and indirect effects of cognitive load, the study aims to contribute to the improvement of online education platforms in terms of user experience. The research was conducted on online courses taken by Akdeniz University students via the Microsoft Teams platform. Cognitive control and flexibility were measured using the Cognitive Control and Flexibility Scale, cognitive load was measured using the NASA-TLX, and the perceieved system usability was determined using the System Usability Scale. The findings show that, as cognitive load increases, perceived system usability decreases; conversely, this perception increases with higher cognitive control and flexibility. Furthermore, it was determined that cognitive load indirectly affects system usability via cognitive control and flexibility. Consequently, online education systems should be designed to reduce users’ cognitive load while supporting their cognitive control and flexibility.