The study reported in this paper investigates the effect of navigational mechanisms on students in a computer based assessment environment at a cross-cultural setting. Literatures in computer based assessment studies highlight the phenomenon of “test mode effect” that can explain the differences in test scores across two different formats of testing. In this study the authors posit that even different formats of presentation through the same media might affect students’ performance in a computer based assessment environment. The study reported here investigates the effect of two different navigational mechanisms namely, vertical menu and step based navigations on students’ performance. Students from Indian universities and American universities participated in the study. The results highlight that navigational mechanisms affect students’ performance and their subjective evaluation of the Computer based Assessment system. The results of the study would provide navigational heuristics for the Graphical User Interface designers to design a learner centered Computer based Assessment system.