In user interface design, pop-up windows are widely used to help direct user attention effectively. The reasonable use of the characteristics of pop-up windows can accurately guide users' attention, emphasize the importance of crucial information, and thus improve users' efficiency in visual-searching and decision-making. This study aims to investigate the effects of the pop-up window position and gender difference on the users' visual search process pertinent to mobile applications. The research variables were the locations of the pop-up window (i.e., at the center and bottom of the screen) and gender difference (i.e., male and female). A total of 40 participants were invited to take part in the experiment via convenience sampling methods. The experiment was a 2 x 2 between-subjects design. The data generated in the experiment were obtained from participants' task performance, questionnaire of System Usability Scale (SUS), participants' subjective evaluations, and post-experiment semi-structured interviews. The results of the study showed that: (1) The main effect of gender difference revealed significant difference in task performance, with males were more likely to find task goals than females. (2) The main effect of the pop-up window position made a significant difference on the System Usability Scale (SUS), with participants' perceived ease-of-use being higher when the window was located in the center of the screen. (3) There were also significant gender difference in users' subjective evaluation pertinent to the pop-up windows. (4) There was a significant interaction effect between the pop-up window position and gender difference on the search task, i.e., when the window was located in the center of the screen, the female performed better than the males. When the pop-up window was at the bottom of the screen, males performed better than females. The research findings can be good design references for the interaction designers in the near future.